The Dundee Resource for Protein Structure Prediction and Sequence Analysis
Lead Research Organisation:
University of Dundee
Department Name: School of Life Sciences
Abstract
This resource application is focused on supporting and maintaining computer tools and techniques developed at the University of Dundee that are in daily use by thousands of biological scientists throughout the UK and the world. The resource will not only ensure that these tools are readily available to all scientists, but also improve the ability of scientists and students to use them through better interfaces and via regular face-to-face training courses and other on-line materials. The tools focus on the analysis of protein sequences and structures which are briefly introduced here. The plans to make a plant, animal or micro-organism are encoded as the molecule DNA and known as its genome. The genome can be represented as a long word made up of four different letters (A, C, G, T). The genome may be a few thousand letters long for a virus, to several billion letters for plants and animals. The genome is divided up into regions called genes which are translated by complex molecular machines into other molecules such as proteins. Humans and other animals have 20-30,000 genes that code for proteins and each protein made up of a sequence of 20 different amino acid types joined together in a chain. Protein sequences from an organism vary in length from a few amino acids, to several thousand and can be represented as a word made up of 20 different letter types. The protein chain folds up into a complex three-dimensional shape that is defined primarily by its sequence. The shape of the protein, its "conformation", dictates the biological function of the protein, so understanding the conformation of a protein is vitally important to understanding the protein function. Over recent years there have been huge advances in technology to sequence DNA and so the genomes of many different organisms have been determined. As a consequence, the sequences of several million proteins are now known but less than 100,000 have had their detailed three-dimensional structures worked out. The computational tools that will make up this resource help to bridge this information gap by classifying protein sequences and making predictions of protein structure that can guide biologists to design more efficient and effective experiments. The main objectives of the proposal are to provide support, maintenance and training for the popular JPred protein structure prediction server which performs up to 95,000 predictions monthly for scientists in 140 countries, the TarO protein sequence analysis suite and Kinomer protein kinase classifier and database. The new resource will integrate these individual tools with a consistent look-and-feel and make them available to researchers and tool developers in new ways over and above a conventional web site. Web sites are good for humans to interact with, but less useful for computer software to interface to. Since our tools are useful for large analyses that might be done on many thousands of proteins, the new resource will also support a novel "web services" interface to the tools. Web services allow a program or application to be run remotely from within a program. For example, I might have a program running on my desktop computer, but call for an intensive calculation to be done on a remote high-performance computer system. We have recently developed a new method to deploy web services (called JABAWS) that makes installation of web services straightforward. A key part of the new resource will be to add more complex applications such as structure prediction to Jabaws and so make them readily available to programmers and end-users
Technical Summary
Although there are many challenges in managing large sequence datasets, the major hurdle is to use the raw sequence data to inform our knowledge and understanding of biological systems. An essential prerequisite to understanding are accurate and reliable software tools to make structural and functional predictions from the sequence data. In this proposal we will build robust support for secondary structure prediction server "JPred" which performs up to 95,000 predictions per month for scientists in 140 countries. We will also build support for the sequence analysis pipeline "TarO" and the protein kinase database and kinase classification pipeline, "Kinomer" by re-engineering all three servers into the new Dundee Resource for Protein Structure Prediction and Sequence Analysis. We will achieve this goal by wrapping components of all three web servers as "web services" in the new Java Bioinformatics Analysis Web Services (JABAWS) system for portable web services. JABAWS will allow programmatic access to the tools that are currently only available through a web page, and also make them accessible to the popular Jalview workbench for visualisation and analysis of protein sequences. JABAWS can also be deployed on a laptop or in the Amazon cloud computing service. Since annotations of complete proteomes are valuable in understanding the function of all proteins coded for by a genome, we will run all the tools developed here on complete proteomes and maintain the results as a database that can be accessed through a web site and DAS (Distributed Annotation Server) server. The users of the new integrated resource will be very diverse, from experimental biologists with little knowledge of computing, to bioinformaticians who write their own software. Accordingly, we will develop extensive manuals and e-learning materials to inform and educate potential users at all levels and we will run regular training courses.
Planned Impact
The Dundee Resource will support a set of tools that will be widely used by the international biological sciences community. This has impact to all areas of academic BBSRC research as well as MRC funded and other research councils that support research involving genome or protein sequences. Users of the Dundee Resource span academia across all biological subject areas and researchers in the pharmaceutical, agrochemical, agricultural and animal breeding industries where the analysis of protein sequences and their functional context is important to the economic success of the company. As such, the Dundee Resource will have both Economic and Societal impacts by speeding up the accuracy and depth of inference possible from sequence data and so increasing the competitiveness of its users in academia and industry. Improved competitiveness of the users of the resource across such a wide range of academic and industrial domains is likely to lead to improved competitiveness for the UK. The new ProteoCache will significantly accelerate the speed at which scientists can access key information about their proteome of choice and apply this in experimental design or interpretation.
The Dundee Resource, particularly when coupled with the Jalview sequence analysis workbench, will also be important in teaching students in life sciences disciplines both basic and advanced sequence analysis. This educational role will enhance the knowledge and expertise of future generations of biologists and technologists working in academia and industry across all molecular life sciences disciplines in the UK.
Further beneficiaries will be attendees at the annual training workshop that will be run to teach potential users both the scientific background to the methods in the Dundee Resource and the practical use of the tools on their specific problems. The training workshops will be open to graduate students, postdocs, academics and members of industry. For those who can't attend the workshops, the on-line e-learning materials will provide similar information backed by informal email support.
The Dundee Resource for Protein Structure Prediction and Sequence Analysis is aimed at accelerating scientific discovery and maximising the benefit of investment in sequence data generation. However, when coupled with visualisations in Jalview some of the tools such as secondary structure and disorder prediction could be explained to schoolchildren and the general public. We have experience of public outreach through the annual "Doors Open Day" at Dundee and through the development of our GenomeScroller exhibit (www.genomescroller.org) that provides an exciting backdrop on which to explain the human genome, how big it is and how much (and how little) is understood about how it functions. In Year 2 of this grant and subsequent years, we will display and explain outputs of the new Dundee Resource alongside GenomeScroller in order to introduce a new audience to the power and excitement of bioinformatics research.
The Dundee Resource, particularly when coupled with the Jalview sequence analysis workbench, will also be important in teaching students in life sciences disciplines both basic and advanced sequence analysis. This educational role will enhance the knowledge and expertise of future generations of biologists and technologists working in academia and industry across all molecular life sciences disciplines in the UK.
Further beneficiaries will be attendees at the annual training workshop that will be run to teach potential users both the scientific background to the methods in the Dundee Resource and the practical use of the tools on their specific problems. The training workshops will be open to graduate students, postdocs, academics and members of industry. For those who can't attend the workshops, the on-line e-learning materials will provide similar information backed by informal email support.
The Dundee Resource for Protein Structure Prediction and Sequence Analysis is aimed at accelerating scientific discovery and maximising the benefit of investment in sequence data generation. However, when coupled with visualisations in Jalview some of the tools such as secondary structure and disorder prediction could be explained to schoolchildren and the general public. We have experience of public outreach through the annual "Doors Open Day" at Dundee and through the development of our GenomeScroller exhibit (www.genomescroller.org) that provides an exciting backdrop on which to explain the human genome, how big it is and how much (and how little) is understood about how it functions. In Year 2 of this grant and subsequent years, we will display and explain outputs of the new Dundee Resource alongside GenomeScroller in order to introduce a new audience to the power and excitement of bioinformatics research.
People |
ORCID iD |
| Geoffrey Barton (Principal Investigator) |
Publications
Britto-Borges T
(2017)
Correction: A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase.
in PloS one
Drozdetskiy A
(2015)
JPred4: a protein secondary structure prediction server.
in Nucleic acids research
Drozdetskiy A
(2015)
JPred4: a protein secondary structure prediction server.
in Nucleic acids research
Glusman G
(2017)
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.
in Genome medicine
Lai YC
(2015)
Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1.
in The EMBO journal
Llabrés S
(2020)
Disease related single point mutations alter the global dynamics of a tetratricopeptide (TPR) a-solenoid domain.
in Journal of structural biology
MacGowan S
(2019)
The Dundee Resource for Sequence Analysis and Structure Prediction
in Protein Science
| Title | 2019: Jalview Youtube Channel: 13 new and updated videos |
| Description | Publicity films, recordings of lectures and narrated training videos explaining how to use the Jalview system and the Dundee Resource for Protein Sequence Analysis and Structure Prediction are published on Vimeo (https://vimeo.com/jalview and Jalview's youtube channel. In 2019, two publicity films and one lecture (originally given by Dr J. B. Procter as part of a U. Dundee taught master's program) were added to the channel, and 10 training videos were updated for the July 2019 Jalview 2.11 software release. |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2019 |
| Impact | Jalview's youtube channel is viewed over 19,000 times annually and 17% of viewers are based int he UK. It had 130 new subscribers in 2019. |
| URL | https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw/ |
| Title | Jalview Abacus |
| Description | As part of Symbiosis, an Art Science collaboration at the University of Dundee between the School of Life Sciences and the Duncan of Jordanstone College of Art and Design, the Jalview and Dundee Resource for Protein Structure Prediction and Sequence Analysis team worked with Mr Luke Wilson, a second year Art and Philosophy student. The outcome was a physical implementation of the biological sequence alignment and visualisation functionality provided by the Jalview desktop application, that embodies the possibilities and limitations of the underlying computational process. |
| Type Of Art | Artefact (including digital) |
| Year Produced | 2015 |
| Impact | The Jalview Abacus was presented at four events. The artefact was first shown at The Symbiosis Exhibition at the Tin Roof Gallery, Dundee, UK, and a digital image submitted as an Art and Biology poster presented at VIZBI 2015 (vizbi.org/Posters/2015/Y10). A second exhibition took place at the BBSRC's 2015 Innovator of the Year Award (http://www.bbsrc.ac.uk/news/events/2015/1503-innovator-of-the-year/). The piece was also shown at ISMB & ECCB 2015 in Dublin, Ireland, and Mr Luke Wilson won the 2015 ISCB Art in Science Award. |
| URL | https://sites.dundee.ac.uk/symbiosis/jalview-abacus/ |
| Description | This grant supports key resources for the biological research community. JPred is a system for predicting the structure of a protein from its amino acid sequence, it is one of the most widely used and accurate methods. Structure prediction is important to help interpret the flood of data coming from DNA sequencing experiments in many different species. This award has led to the development of improvements to the web server for this predictor and improved its functions and accuracy. The predictor has also been made 10x faster and new ways of accessing the method implemented. As a consequence, JPred now performs up to 500,000 predictions/month for users in around 200 countries. The award also supported the development of JABAWS 2.2 a new webservices system that supports 8 multiple alignment methods, four disorder predictors, 18 conservation calculation methods and and RNA secondary structure predictor. Together, these provide a flexible toolkit for reseachers to explore the structure and function of proteins and RNA. The importance of the resources supported by this award was recognised in 2016 by the award of Elixir-UK resource status as part of the Europe-wide bioinformatics resource network. This made the resource one of only 9 awarded in the UK. |
| Exploitation Route | The results of our work are being used across many fields as recognised by the high usage of the servers and citations in excess of 5,000 for the core papers describing the work. |
| Sectors | Agriculture Food and Drink Education Environment Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| URL | http://www.compbio.dundee.ac.uk |
| Description | Biomedical Resources Fund |
| Amount | £842,437 (GBP) |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2014 |
| End | 09/2019 |
| Description | The Dundee Resource for Sequence Analysis and Structure Prediction (DRSASP) - 2023 and Beyond |
| Amount | £691,611 (GBP) |
| Funding ID | BB/X018628/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2023 |
| End | 08/2027 |
| Description | The Jalview Resource for Biological Sequence, Structure and Function Analysis: 2019 and Beyond |
| Amount | £1,000,000 (GBP) |
| Funding ID | 218259/Z/19/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 12/2025 |
| Title | 14-3-3-Pred PDB (Human) |
| Description | 14-3-3 binding-site predictions for the set of human sequences in PDB from the DRSASP resource 14-3-3Pred. 1,941 representative PDB chains received at least one positive prediction. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | This dataset is integrated into the PDBe-KB knowledge graph and so will reach a wide audience. It is one of only three protein binding-site predictors included in FunPDBe and so is critical to bringing this type of annotation to the PDBe-KB neo4j graph databaseIt is too early to tell what wider impact it will have. |
| URL | http://ftp.ebi.ac.uk/pub/databases/pdbe-kb/annotations/14-3-3-pred/ |
| Title | Domain position missense enrichment score |
| Description | We developed a strategy to score alignment columns by calculating their relative enrichment for human population missense variants. The score is interpreted similarly to evolutionary conservation. This score is akin to the whole gene essentiality metrics calculated by others using population variation data only ours resolves individual protein positions. |
| Type Of Material | Data analysis technique |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | This analysis technique underpins our research into how human genetic variants are distributed in proteins with respect to protein structure and conservation. |
| Title | Domain position structural feature analysis |
| Description | We developed an approach to quantitatively assess the structural properties of an alignment column. Structural features are normally assessed on a per structure basis. Our method allows simultaneous consideration of multiple structures for a single protein and multiple proteins with a structure in an alignment. We can then apply criteria to define domain positions (i.e., alignment columns) as interacting (e.g., with a ligand or protein), buried, helical, etc. |
| Type Of Material | Data analysis technique |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | This technique underpins our research into how human genetic variants are distributed in proteins with respect to protein structure and conservation. |
| Title | OB-Score Pfam 31.0 |
| Description | We calculated OB-Scores for 30,498,342 sequences across 16,449 families from Pfam 31.0. The OB-Score is one of the crystallisation propensity predictors available from DRSASP. These scores are useful to those looking to select representatives of Pfam domains for crystallisation experiments. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | We created this dataset at the request of a peer reviewer of the DRSASP Protein Science 2020 paper. The dataset was announced in this paper (early-2020) and we are checking citations to assess impact. |
| URL | http://www.compbio.dundee.ac.uk/xtal/ob_datasets/ |
| Title | Pfam-ClinVar |
| Description | This dataset contains all ClinVar variants mapped to Pfam domains. The data are currently stored as Python pickles of Pandas DataFrames. Aggregated data are stored as CSV files. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | This database underpins our research into how human genetic variants are distributed in proteins with respect to protein structure and conservation. |
| Title | Pfam-PDB |
| Description | We mapped residue contact data calculated from 17.1K crystal structures in the Protein DataBank (PDB) to 14.5K domains (46%) across 2.5K Pfams (42% of Pfams). These structures covered over 1.5 million residues. The database also contains contact information calculated with our own ProIntVar software and the Arpeggio software from the Blundell group. These data include 76,155 residue-ligand interactions with ligands in the Biolip database (to 21,708 unique residues) and 463,600 inter-domain interactions (to 69,757 unique residues). The data are currently stored as Python pickles of Pandas DataFrames. Aggregated data are stored as CSV files. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | This database underpins our research into how human genetic variants are distributed in proteins with respect to protein structure and conservation. |
| Title | Pfam-gnomAD |
| Description | This data collection contains human population variants from the Genome Aggregation Database (gnomAD; including 2.2 million missense variants) mapped to 31.5K Pfam domains from 5.8K Pfams (35% of Pfam). The domains span almost 14.5K unique proteins (71% of human proteins in the UniProtKB/SwissProt) and cover over 3.5 million residues (31% of human residues in SwissProt). n.b. these percentages are almost equivalent to the coverage of the known human proteome. The data are currently stored as Python pickles of Pandas DataFrames. Aggregated data are stored as CSV files. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | This database underpins our research into how human genetic variants are distributed in proteins with respect to protein structure and conservation. |
| Title | ProteoCache |
| Description | ProteoCache is a database containing precomputed results of DRSASP and other applications for whole proteomes built with Apache Cassandra together with a Node.js API based on DataStax's cassandra-driver. The database contains JPred4 predictions (including full alignments and PSI-BLAST profiles) for most of the Human (57,823 sequences; 78%), S. cerevisiae S288C (5,049; 83%), and E. coli K-12 (4,144; 94%) UniProt reference proteomes as well as disorder predictions for 79,513 sequences from the four disorder predictors provided by JABAWS. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | No |
| Impact | JPred4 interfaces with ProteoCache to improve the performance of JPred4 for previously run sequences. Our goal is that all DRSASP applications will similarly interface with the ProteoCache to improve performance of our web services. The ProteoCache itself will in the future be able to serve bulk downloads of whole proteomes or other large selections of sequences and also permit complex queries over the data. We have served an individual request for JPred4 predictions for the human proteome from the ProteoCache. n.b. ProteoCache is not presently directly accessible to external users but results are served from it via JPred. |
| Description | Collaboration with Anton van der Merwe, Oxford |
| Organisation | University of Oxford |
| Department | Sir William Dunn School of Pathology |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Collaboration on the analysis of SARS-CoV2 spike/ACE2 interactions by computational and experimental methods |
| Collaborator Contribution | We identified the most functionally interesting variants in ACE2 and the RBD by computational methods, then provided these to our collaborators for complementary experiments. We then discussed the results and conclusions. |
| Impact | No outputs yet, we are still doing experiments and calculations. |
| Start Year | 2020 |
| Description | Collaboration with Genentech USA on the application and development of the Slivka webservices solution |
| Organisation | Genentech, Inc |
| Country | United States |
| Sector | Private |
| PI Contribution | We have developed Slivka which is a flexible open source webservices solution. Genentech USA have adopted this for their internal use and have collaborated with us on its continued development. |
| Collaborator Contribution | Deployment and testing of Slivka in a commercial environment. Implementation of >30 applications within the Slivka environment. Collaboration on testing the system in the Genentech environment. Collaboration on writing a publication about the system. Providing a simple web interface to the Slivka back-end. |
| Impact | none at present but a publication is in prepartation for submission in 2024 |
| Start Year | 2021 |
| Description | Dr Yann Ponty (CNRS,LIX) - Integrated visualisation of RNA multiple alignment and secondary structure visualisation tools |
| Organisation | Ecole Polytechnique |
| Country | France |
| Sector | Academic/University |
| PI Contribution | Provided remote supervision and support for student software developers based in Dr Ponty's research group and elsewhere to integrate Dr Ponty's VARNA visualisation tool into the Jalview platform. |
| Collaborator Contribution | Dr Ponty provided scientific and technical guidance on the integration of VARNA and the extension of Jalview to support RNA secondary structure visualisation and analysis. |
| Impact | Enhancements to the Jalview platform were developed as a result of the collaboration: Software - 2012: Version 2.8: The Jalview Multiple Sequence Analysis and Visualisation Workbench (2012) https://app.researchfish.com/getform/0/technical-products/56ddb84b8f3865.12672428/view?action=viewdetails&name=56ddb84b8f3865.12672428 |
| Start Year | 2011 |
| Description | Improving the portability of JPred with a Docker container |
| Organisation | Bristol-Myers Squibb |
| Department | Celgene |
| Country | United States |
| Sector | Private |
| PI Contribution | Dr Stuart MacGowan provided the JPred application source code and datasets and an instructional overview of the application architecture. |
| Collaborator Contribution | Dr Alejandro Panjkovich (Celgene) built a Docker container for the JPred pipeline from the JPred source code and datasets. Dr Panjkovich has started to test the Docker version by comparing the JPred predictions to those obtained from the web server. |
| Impact | JPred-Portable |
| Start Year | 2019 |
| Description | PDBe-KB and FunPDBe |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Prof Geoff Barton, Dr James Procter, Dr Stuart MacGowan and Dr Fábio Madeira participated in the PDBe-KB FunPDBe working group meetings and workshops. Dr MacGowan was consulted to provide requirements for the FunPDBe JSON schema. Dr MacGowan and Dr Madeira wrote code to format DRSASP resource output for compliance with the FunPDBe JSON schema. Dr Stuart MacGowan uploaded 14-3-3 binding-site predictions for all human protein structures in the PDB. These were calculated with the DRSASP resource 14-3-3-Pred and formatted to FunPDBe JSON format. |
| Collaborator Contribution | The PDBe-KB and FunPDBe team (key contacts: Sameer Velankar and Mihaly Varadi) built the PDBe-KB Neo4j database, web APIs, and web pages and the FunPDBe deposition and porting pipelines. They coordinated overall project delivery and organised working group meetings. |
| Impact | PDBe-KB: a community-driven resource for structural and functional annotations 14-3-3-Pred PDB Annotations |
| Start Year | 2017 |
| Title | 2013: JABA Web Services |
| Description | Jabaws is a Java web services stack that is portable and so easy for end-users to install. The stack comes with a collection of popular methods for multiple sequence alignment as well as methods for protein disorder prediction and amino acid conservation calculation. The JABAWS installation may run on a Linux machine with a computer cluster attached, or alternatively in a virtual machine that runs on a laptop or desktop computer. The JABAWS distribution includes a command-line client to allow bioinformaticians to program scripts against it. However, its most important use is as the web services back-end for the Jalview multiple alignment workbench (www.jalview.org). The JABAWS installation at Dundee performs around 10,000 alignments a month for users world-wide. Installations also exist at other locations in the world, including in companies, but we cannot gather full statistics on their usage. |
| Type Of Technology | Software |
| Year Produced | 2013 |
| Open Source License? | Yes |
| Impact | This is actually a continuous output as JABAWS continues to be maintained and developed as part of the award. JABAWS web services are used by thousands of scientists across a broad range of fields so the impact is very broad. |
| URL | http://www.compbio.dundee.ac.uk/jabaws |
| Title | 2014: JPred4 |
| Description | JPred4 is the latest development of our methods for protein secondary structure prediction. The JPred4 website has been completely updated to exploit current web technology standards, there have been significant improvements to the accuracy of the underlying algorithm and changes have been made to the output to interface more effectively with the Jalview multiple sequence analysis workbench. In addition a new programmable interface makes it easier for end-users to carry out large numbers of predictions (e.g. for entire proteomes) and return the results in a convenient format. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2014 |
| Impact | The new developments to the JPred4 web resource have increased the number of predictions carried out per month from around 10,000 on average to up to 250,000. The server is used by scientists in over 170 countries. A paper was published in 2015 on the new developments and this has so far been cited 40 times (Since July 2015 - I am writing this in March 2016.). |
| URL | http://www.compbio.dundee.ac.uk/jpred |
| Title | 2015: ProteoCache |
| Description | The ProteoCache is a high-performance database built using NoSQL technology on the Cassandra framework. It stores the results of the JPred4 prediction engine (www.compbio.dundee.ac.uk/jpred4) and further analysis results on proteins are being added to it as time progresses. The first release of the ProteoCache went live in July 2015 as the back-end cache for the JPred4 prediction server. At the time I write this, the ProteoCache now has over 400,000 predictions stored together with all associated data and around 30% of requests to the JPred4 server are now returned from the cache in seconds rather than calculated again in minutes to hours per prediction. As each new sequence is submitted to the server, the results are added to the cache and so quickly available should a request be made for the identical sequence. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2015 |
| Impact | The ProteoCache has enabled a much higher throughput to be maintained for our leading secondary structure prediction server with minimum investment in new computer hardware and hence impact on greenhouse emissions! |
| Title | 2018: Version 2.10.4: The Jalview Multiple Sequence Analysis and Visualisation Workbench |
| Description | Jalview, is generally agreed to be the most widely used program for visualising sequence alignments and editing them. It is installed on over 70,000 computers world-wide, on hundreds of thousands of web pages, and in daily use by thousands of scientists and students. Although other programs exist to visualise and edit multiple alignments, Jalview not only allows alignments to be viewed coloured and edited, but also exploits the internet to connect to over 1000 sources of sequences and complex annotations on those sequences. In addition, Jalview exploits state-of-the-art internet technology to connect to computer servers that can perform large calculations on the sequences and return these to the user in a few seconds or minutes. In this way the program puts a mass of human knowledge at the fingertips of the scientist and so saves them a huge amount of time in exploring the function of their favourite protein, DNA or RNA molecule. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Briefly describe any notable impacts resulting from the development of this software or technical product. * Jalview has wide reaching impact - it is started at least 250,000 times per year by scientists in over 160 countries and the two publications describing Jalview have been cited in excess of 5,500 times (Google Scholar Citations). Jalview is used by scientists in virtually all fields of modern biology and biomedicine where biological sequences are analysed and compared. |
| URL | http://www.jalview.org/development/release-history/Jalview-2104 |
| Title | 2018: Version 2.10.4b1: The Jalview Multiple Sequence Analysis and Visualisation Workbench |
| Description | Jalview, is generally agreed to be the most widely used program for visualising sequence alignments and editing them. It is installed on over 70,000 computers world-wide, on hundreds of thousands of web pages, and in daily use by thousands of scientists and students. Although other programs exist to visualise and edit multiple alignments, Jalview not only allows alignments to be viewed coloured and edited, but also exploits the internet to connect to over 1000 sources of sequences and complex annotations on those sequences. In addition, Jalview exploits state-of-the-art internet technology to connect to computer servers that can perform large calculations on the sequences and return these to the user in a few seconds or minutes. In this way the program puts a mass of human knowledge at the fingertips of the scientist and so saves them a huge amount of time in exploring the function of their favourite protein, DNA or RNA molecule. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Jalview has wide reaching impact - it is started at least 250,000 times per year by scientists in over 160 countries and the two publications describing Jalview have been cited in excess of 5,500 times (Google Scholar Citations). Jalview is used by scientists in virtually all fields of modern biology and biomedicine where biological sequences are analysed and compared. |
| URL | http://www.jalview.org/development/release-history/Jalview-2104b1 |
| Title | 2018: Version 2.10.5: The Jalview Multiple Sequence Analysis and Visualisation Workbench |
| Description | Jalview, is generally agreed to be the most widely used program for visualising sequence alignments and editing them. It is installed on over 70,000 computers world-wide, on hundreds of thousands of web pages, and in daily use by thousands of scientists and students. Although other programs exist to visualise and edit multiple alignments, Jalview not only allows alignments to be viewed coloured and edited, but also exploits the internet to connect to over 1000 sources of sequences and complex annotations on those sequences. In addition, Jalview exploits state-of-the-art internet technology to connect to computer servers that can perform large calculations on the sequences and return these to the user in a few seconds or minutes. In this way the program puts a mass of human knowledge at the fingertips of the scientist and so saves them a huge amount of time in exploring the function of their favourite protein, DNA or RNA molecule. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Jalview has wide reaching impact - it is started at least 250,000 times per year by scientists in over 160 countries and the two publications describing Jalview have been cited in excess of 5,500 times (Google Scholar Citations). Jalview is used by scientists in virtually all fields of modern biology and biomedicine where biological sequences are analysed and compared. |
| URL | http://www.jalview.org/development/release-history/Jalview-2105 |
| Title | Code for functional annotation of DRSASP resources in FunPDBe |
| Description | FM_FunPDBe Scripts for adding functional annotations to FunPDBe. How to use Getting Fasta sequences from a list of PDB ids Extracting the sequences from all chains in the PDB files $ python extract_sequences.py data/funpdbe_examples_list.txt data/funpdbe_examples_list.fasta Getting Fasta sequences from PDB/CHAIN or UniProt IDs Extracting the sequence from all chains based on a PDB ID $ python extract_sequences.py --pdb Extracting the sequence from all chains based on a PDB ID and Chain ID $ python extract_sequences.py --pdb --chain Extracting the sequence from all PDB/Chain IDs based on a UniProt ID $ python extract_sequences.py --uniprot Running Barton Group Predictors on a collection of Fasta sequences Running NOD $ python run_predictors.py nod data/funpdbe_examples_list.fasta Running 14-3-3-Pred $ python run_predictors.py 1433pred data/funpdbe_examples_list.fasta Running Jpred $ python run_predictors.py jpred data/funpdbe_examples_list.fasta Scoring and Classifier Thresholds NOD NOD - Artificial Neural Network (20-length sequence windows with a score cut-off >= 0.8) 14-3-3-Pred ANN - Artificial Neural Network (cut-off >= 0.55) PSSM - Position-Specific Scoring Matrix (cut-off >= 0.80) SVM - Support Vector Machine (cut-off >= 0.25) Consensus - Average of the scores provided by the three methods (cut-off >= 0.50) Dependencies Using Python 3.5+. Check requirements.txt for all Python dependencies. Other Dependencies: NOD requires batchman from SNNS package to be installed. See http://www.compbio.dundee.ac.uk/www-nod/downloads.jsp for more details. 14-3-3-Pred requires PyML. See http://pyml.sourceforge.net/index.html for more on how to install it. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | This allows annotations to be submitted to the FunPDBe database. |
| URL | https://github.com/bartongroup/FM_FunPDBe |
| Title | pyDRSASP: VarAlign, ProIntVar and ProteoFAV |
| Description | This software simplifies the complex task of connecting the heterogeneous data derived from variants, protein sequences, protein structures, and multiple sequence alignments and is essential to our work on how human genetic variants are distributed in proteins with respect to protein structure and conservation. Our approach is to represent the data as Pandas DataFrames. Once all these data are harmonized, we can conduct complex queries and aggregations. For example, "return all missense variants at residues where the position is conserved and involved in a hydrogen bond with a ligand in Pfam PF00001" and "count all missense variants in each alignment column of PF00017". This software is being developed as a series of Python modules, and we will release the libraries and provide a web service through Slivka this year. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Impact | These tools are core resources for several postgraduate students in the Barton group (2 PhDs, 2 postgraduate rotations and 2 honours projects) and are also being used by other groups in the Division of Computational Biology here at Dundee. The tools enable these users to calculate residue level human population constraint for their proteins of interest and to assess this, and other features like conservation, in the context of alignment level structural analyses. |
| Description | 2010 July Poster and ISMB Technology track talk: Jalview: Past, Present and Future. (Boston, US) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Jalview 2.5 and the newly developed JABAWS platform for bioinformatics web services were presented as posters and described during a 30 minute ISMB Technology track in Boston at ISMB 2010. The presentation highlighted future development goals and identified key technologies that would be leveraged in future releases of the software. It also provided an opportunity to engage with teams from related projects around the world. |
| Year(s) Of Engagement Activity | 2010 |
| URL | http://www.iscb.org/uploaded/css/56/18507.pdf |
| Description | 2011 Poster and ECCB/ISMB Technology track talk: Jalview 2.7. ECCB/ISMB 2011 (Vienna, Austria) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A poster and 30 minute technology track talk was delivered by Dr James Procter at the joint ISMB and European Conference on Computational Biology meeting in Vienna, 2011. The talk presented new developments in version 2.7 of the Jalview system, as well as improvements in infrastructure and source code management. Interactions with other delegates lead to future training course engagements. |
| Year(s) Of Engagement Activity | 2011 |
| URL | http://www.iscb.org/uploaded/css/82/22491.pdf |
| Description | 2013 Jalview and JABA Training course at University of Oxford |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | By running training courses we ensure that the next generation of users of our software can gain maximum benefit from it. The courses are run for up to 30-40 people for up to 3 days depending on the constraints of the venue and demand. People on our courses are Ph.D. students, post-docs, Principal Investigators and various levels of Industry. We are funded on BB/G022682/1, BB/J019364/1 and BB/L020742/1 to do training and outreach associated with our awards. |
| Year(s) Of Engagement Activity | 2013 |
| URL | http://www.jalview.org/training/training-courses |
| Description | 2013 Jalview training course |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | By running training courses we ensure that the next generation of users of our software can gain maximum benefit from it. The courses are run for up to 30-40 people for up to 3 days depending on the constraints of the venue and demand. We are funded on BB/G022682/1, BB/J019364/1 and BB/L020742/1 to do training and outreach associated with our awards. |
| Year(s) Of Engagement Activity | 2013 |
| URL | http://www.jalview.org/training/training-courses |
| Description | 2013 Jalview training course at EBI Hinxton |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | By running training courses we ensure that the next generation of users of our software can gain maximum benefit from it. The courses are run for up to 30-40 people for up to 3 days depending on the constraints of the venue and demand. People on our courses are Ph.D. students, post-docs, Principal Investigators and various levels of Industry. We are funded on BB/G022682/1, BB/J019364/1 and BB/L020742/1 to do training and outreach associated with our awards. |
| Year(s) Of Engagement Activity | 2013 |
| URL | http://www.jalview.org/training/training-courses |
| Description | 2013 July BOSC 2013 Ten rules for open source software development. Bioinformatics Open Source Conference (BOSC) at ISMB 2013, Berlin, Germany. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Procter presented and sat on a panel discussion covering themes raised in the article in PLOS Computational Biology: Ten Simple Rules for the Open Development of Scientific Software, alongside Dr Andreas Prlic (UCSD), and Dr Hilmar Lapp (NESCeNT, US). |
| Year(s) Of Engagement Activity | 2013 |
| URL | http://www.open-bio.org/bosc2013/day1/BOSC2013_TenSimpleRules_-_Prlic_Procter_Lapp.pdf |
| Description | 2013 July ISMB Technology Track: Extensible open source sequence analysis with Jalview and JABAWS. ISMB & ECCB 2013, Berlin, Germany. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr James Procter presented a 30 minute presentation as part of the ISMB 2013 ISMB Technology Track, where the key features of the Jalview platform and JABAWS web services system were described, including latest developments for annotation of alignments with 3D structure data and services for alignment based RNA and Protein secondary structure prediction. Prof. Geoff Barton and Dr Procter also held a Jalview and JABAWS 'Birds of a feather' to discuss future developments with Jalview users and service providers present at the conference. |
| Year(s) Of Engagement Activity | 2013 |
| URL | http://www.jalview.org/Community/Community-news/Jalview-talk-and-users-meeting-in-Berlin-at-ISMB-201... |
| Description | 2014 Dec "Jalview" Tool talk at BiVi 2014 - The1st UK BBSRC Biological Visualisation Network AGM, Edinburgh Napier, UK. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The 1st Annual General Meeting of the BBSRC UK Biological Visualisation Network brought together biological data visualisation software developers, computer scientists, computational biologists from around the UK. Dr James Procter presented a talk and poster describing the key features and data visualisation capabilities of Jalview, highlighting key capabilities that have lead to it becoming a widely used tool in teaching and research. Engagement with other delegates at the meeting not only identified opportunities for improvements to Jalview, but also highlighted best practices and future challenges in research software engineering and biological visualisation design. |
| Year(s) Of Engagement Activity | 2014 |
| URL | http://bivi.co/presentations/field_event_ref/477 |
| Description | 2014 Jalview and JABA training course, Dundee (April) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | By running training courses we ensure that the next generation of users of our software can gain maximum benefit from it. The courses are run for up to 30-40 people for up to 3 days depending on the constraints of the venue and demand. People on our courses are Ph.D. students, post-docs, Principal Investigators and various levels of Industry. We are funded on BB/G022682/1, BB/J019364/1 and BB/L020742/1 to do training and outreach associated with our awards. |
| Year(s) Of Engagement Activity | 2014 |
| URL | http://www.jalview.org/training/training-courses |
| Description | 2014 Jalview and JABA training course, Dundee (October) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | By running training courses we ensure that the next generation of users of our software can gain maximum benefit from it. The courses are run for up to 30-40 people for up to 3 days depending on the constraints of the venue and demand. People on our courses are Ph.D. students, post-docs, Principal Investigators and various levels of Industry. We are funded on BB/G022682/1, BB/J019364/1 and BB/L020742/1 to do training and outreach associated with our awards. |
| Year(s) Of Engagement Activity | 2014 |
| URL | http://www.jalview.org/training/training-courses |
| Description | 2014 Jalview and JABA training course, UCL, London. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | By running training courses we ensure that the next generation of users of our software can gain maximum benefit from it. The courses are run for up to 30-40 people for up to 3 days depending on the constraints of the venue and demand. People on our courses are Ph.D. students, post-docs, Principal Investigators and various levels of Industry. We are funded on BB/G022682/1, BB/J019364/1 and BB/L020742/1 to do training and outreach associated with our awards. |
| Year(s) Of Engagement Activity | 2014 |
| URL | http://www.jalview.org/training/training-courses |
| Description | 2014 July ISMB Technology Track: Protein and RNA alignment and analysis with Jalview 2.8.2 and JABAWS 2.1. ISMB 2014, Boston USA. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A 30 minute seminar was delivered as part of the International Society for Computational Biology (ISCB)'s 22nd Intelligent Systems in Molecular Biology (ISMB) conference's technology track. ISMB 2014 attracted computational biologists, bioinformaticians and other computer scientists engaged in research, teaching and training, as well as post-graduate students and early career researchers. The seminar highlighted new 3D structure annotation and visualisation capabilities in Jalview, and an update to the JABAWS platform for bioinformatics analysis web services provided by the Dundee Resource for Protein Structure Prediction and Sequence Analysis. As a US based meeting, it particularly facilitated engagement with academic and industrial researchers and educators who use Jalview and JABAWS resources in teaching and research. |
| Year(s) Of Engagement Activity | 2014 |
| URL | http://www.iscb.org/uploaded/css/166/30122.pdf |
| Description | 2014 Protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis with Jalview |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | By running training courses we ensure that the next generation of users of our software can gain maximum benefit from it. The courses are run for up to 30-40 people for up to 3 days depending on the constraints of the venue and demand. People on our courses are Ph.D. students, post-docs, Principal Investigators and various levels of Industry. This particular course was run over three days and introduced new material about the JPred4 prediction server that had not previously formed part of one of our training courses. We are funded on BB/G022682/1, BB/J019364/1 and BB/L020742/1 to do training and outreach associated with our awards. |
| Year(s) Of Engagement Activity | 2014 |
| URL | http://www.jalview.org/training/training-courses |
| Description | 2015 July ISMB Technology Track: Biomolecular sequence analysis with Jalview and JPred4. 1hr technology track. ISMB & ECCB 2015, Dublin, Ireland. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A one hour seminar was delivered as part of the joint International Society for Computational Biology (ISCB) and Intelligent Systems in Molecular Biology (ISMB) and European Conference on Computational Biology (ECCB) conference's technology track. ISMB and ECCB meetings attract a broad range of computational biologists, bioinformaticians and other computer scientists engaged in research, teaching and training, as well as post-graduate students and early career researchers. The seminar highlighted updates to the Jalview software system, and the Dundee Resource for Protein Structure Prediction and Sequence Analysis' JPred4 server. It also provided a valuable opportunity to engage with users of these systems, and those who employ these systems for educational purposes. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www.iscb.org/uploaded/css/194/32658.pdf |
| Description | 2015: Jalview Online Training YouTube Channel - 5 videos created |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The Jalview online Training YouTube channel was created to provide video guides on how to use Jalview (www.jalview.org) for different tasks. In the period 2015-March 2017, the Channel has had over 20,000 plays by users from all over the world. |
| Year(s) Of Engagement Activity | 2015 |
| URL | https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw |
| Description | 2015: Protein and RNA multiple sequence alignment, protein secondary structure prediction, trees, sub-family and function analysis with Jalview |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA. Register via the University of Cambridge website. Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication. The course involves of a mixture of talks and hands-on exercises. Day 1 is an introduction to protein multiple sequence alignment editing and analysis with Jalview. Day 2 focuses on using Jalview for RNA sequence analysis, and also integrating cDNA and protein analysis and covers more advanced applications after lunch. Day 3 concentrates on protein secondary structure prediction with JPred version 4 as well as protein sub-family analysis to identify functionally important residues. There will be opportunities for attendees to get advice on analysis of their own sequence families. Target audience: Graduate students, Postdocs and Staff members from the University of Cambridge, Affiliated Institutions and other external Institutions or individuals Further details regarding eligibility criteria are available here Further details regarding the charging policy are available here Session: Date Time Venue Trainer Mon 11 May 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site James Procter , Geoff Barton , Suzanne Duce Tue 12 May 09:30 - 17:30 Bioinformatics Training Room, Craik-Marshall Building, Downing Site James Procter , Geoff Barton , Suzanne Duce Wed 13 May 09:00 - 16:00 Bioinformatics Training Room, Craik-Marshall Building, Downing Site Geoff Barton , James Procter , Suzanne Duce Format: Presentations, demonstrations and practicals Course Materials: http://www.jalview.org/tutorial/training-materials/2015/Cambridge/May/ Start Date: 11-05-2015 to 13-05-2015 location: Craik-Marshall Building, Downing Site, University of Cambridge Links: Register via the University of Cambridge website Duration: 3 days |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www.jalview.org/training/training-courses/Protein-and-RNA-multiple-sequence-alignment-protein... |
| Description | 2016 Jalview Glasgow 2016 One Day Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Protein, RNA and DNA multiple sequence alignment and functional analysis workshop using Jalview This one day computer based hands-on training course is designed for life sciences graduate students and researcher scientists who works with proteins, RNA and DNA sequence data. The course will involve presentations, hands-on exercises and demonstrations. Plus, there are opportunities during the day to discuss your own analysis problems with the Jalview developers. Participants are given a Jalview training manual. The course is suitable for both Jalview novices and experienced users who would like to learn more about Jalview's capabilities. The course is on Friday 14th October from 9.15am - 5.00pm in the Strathclyde Institute of Pharmacy and Biomedical Sciences, Room CV309b, Coville Building, 16 Richmond Street, Glasgow G1 1XQ. Course Aims: to provide training in how to use Jalview multiple sequence alignment visualisation program to visualise proteins, RNA and DNA data. Course materials: http://www.jalview.org/tutorial/training-materials/2016/Glasgow/ Learning topics: Introducing Jalview and its capabilities Launching Jalview from a web browser Loading, editing and saving sequences and alignments Selecting and creating groups Colouring sequences and figure generation Undertaking multiple sequence alignment, Viewing annotation and features PCA and tree analysis Working with 3D structures Protein prediction analysis Working with RNA sequences and integrating cDNA and protein analysis Time: 9.15am - 5.00pm |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.jalview.org/training/training-courses/Jalview-Glasgow-2016-One-Day-Workshop |
| Description | 2016 SLS Postgrad Computational Training at University of Dundee |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | 2016 SLS Postgrad Computational Training Multiple Sequence Alignment and Analysis with Jalview This workshop course employs talks and hands-on exercises to help students start using the versatile protein and nucleic acid alignment and visualisation software Jalview (developed within the School of Life Sciences). Over two sessions, we will cover launching Jalview, accessing sequence, alignment and 3D structure databases, creating, editing and analysing alignments, phylogenetic trees, visualisation of 3D structure data, and preparation of figures for presentation and publication. Wednesday afternoons 13.00 to 17.00 on 3rd and 10th February, Dalhousie 1G16 ITS 3 Protein Sequence Analysis The aim of this workshop is to give an understanding of how best to use computational methods to "make sense" of the structure and function of your favourite protein. The workshop will introduce the principles of sequence analysis and its relationship to protein structure and function. It will highlight common methods and tools for protein sequence analysis and multiple sequence alignment will be explained. The workshop will include hands-on examples of methods that exploit evolutionary information to predict structural features from sequence and to identify functionally important residues by sub-family analysis. Prerequisites: 'Multiple Sequence Alignment and Analysis with Jalview'. If you can, please bring a well-specified laptop with you to the session and make sure it runs Jalview. Wednesday afternoons 13.00 to 17.00 on 17th and 24th February, Dalhousie 1G16 ITS 3 Start Date: 03-02-2016 to 24-02-2016 location: Dalhousie 1G16 ITS 3, University of Dundee Duration: 4 weeks |
| Year(s) Of Engagement Activity | 2012,2016 |
| URL | http://www.jalview.org/training/training-courses/2016-SLS-Postgrad-Computational-Training |
| Description | 2016 SLS Postgraduate training in computational biology - Jalview, protein structure prediction and sub-family analysis |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | By running training courses we ensure that the next generation of users of our software can gain maximum benefit from it. The courses are run for up to 30-40 people for up to 3 days depending on the constraints of the venue and demand. This course was run over four days as part of our Ph.D. training programme, but was also attended by postdoctoral staff and group leaders. People on our courses are Ph.D. students, post-docs, Principal Investigators and various levels of Industry. We are funded on BB/G022682/1, BB/J019364/1 and BB/L020742/1 to do training and outreach associated with our awards. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.jalview.org/training/training-courses |
| Description | 2016 Sept - Jalview booth with videos and demos as part of the first Coding Expo at The Mary Erskine School, Edinburgh, UK |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Mary Erskine School in Edinburgh staged a Coding Expo, an exhibition style event in the school hall with stalls for different presenters. Pupils could visit each stall and talk to industry and academia volunteers about their work and how computing contributed to it. The aims were to highlight the diversity of technology-related professionals, raise awareness about the school's plan to offer National 5 Computing Science in 2017, and gauge interest from pupils for a lunchtime 'Coding Club'. Dr Kira Mourão hosted a stall showing Jalview videos, and delivered a very popular hands-on demonstration using Jalview to analyse one of the proteins that makes up bones, osteocalcin, to understand how the protein has changed in modern humans compared with neanderthal and other primates. Dr Mourão raised awareness of Jalview and computational biology with the pupils and biology staff at the school through informal discussion. The event overall was also judged by the school to be very successful, and resulted in 54 signups for the new Code Club. |
| Year(s) Of Engagement Activity | 2016 |
| Description | 2016: Jalview Online Training YouTube Channel - 20 Videos created |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The Jalview online Training YouTube channel was created to provide video guides on how to use Jalview (www.jalview.org) and the Dundee Resource for different tasks. In the period 2015-March 2017, the Channel has had over 20,000 plays by users from all over the world. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw/featured |
| Description | 2017 - May - Jalview 'Tips and Tricks' Tutorial as part of the 3rd UK Biological Visualisation Network Annual General Meeting |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A two hour workshop on experimental and technical aspects of the Jalview workbench for Multiple Sequence Alignment and Analysis was conducted on the 3rd Annual General Meeting of the UK Biological Visualisation Network's training day to a group of biological data visualisation researchers and practitioners. Aspects of this workshop included discussion about workarounds for technical limitations of existing web APIs for public datasets, and future web platform development directions in partnership with other ELIXIR-UK node resources. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://bivi.co/page/3rd-bivi-annual-meeting-workshops#jalview |
| Description | 2017 Dunfermine High School's 'Routes into Employment' Networking event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Kira Mourão gave a talk about how she became a software developer at Dunfermline High School's 'Routes into Employment' networking event for S2 pupils. She also gave a short Jalview demonstration and explained how software developers work with scientists to build tools to help them do research. |
| Year(s) Of Engagement Activity | 2017 |
| Description | 2017 February - One day workshop at University of St. Andrews on Jalview and investigating the structure and function of Proteins, RNA and DNA |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Dr James Procter and Dr Suzanne Duce were invited by the Bioinformatics Unit of St Andrews Medical Sciences to hold a one day training course for post-doctoral researchers and PhD students in medicine, biology and ecology. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.jalview.org/training/training-courses/St-Andrews-2017-One-Day-Workshop |
| Description | 2017 February - Postgraduate Training at the University of Dundee: Multiple Sequence Alignment and Analysis with Jalview |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | 33 postgraduate students and researchers from University of Dundee and Strathclyde University attended a one day Jalview hands on training course delivered by Dr James Procter and Dr Suzanne Duce. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.jalview.org/training/training-courses/Multiple-Sequence-Alignment-and-Analysis-with-Jalvi... |
| Description | 2017 July - ISMB Technology Track Talk: Jalview and the Dundee Resource for Sequence Analysis and Structure Prediction at ISMB/ECCB Conference 2017 Prague, Czech Republic |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A 30 minute talk presenting the latest developments in the Dundee Resource for Protein Structure Prediction and Jalview was given as part of The International Society for Computational Biology (ISCB)'s 25th Intelligent Systems in Molecular Biology (ISMB) conference's technology track. The talk highlighted capabilities provided by the Dundee Resoource for Protein Structure Prediction and features introduced in new releases of the JABAWS server for multiple sequence alignment and analysis, and the Jalview desktop application. It also showcased online videos and training materials for the Dundee Resource and Jalview. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.iscb.org/uploaded/css/222/38588.pdf |
| Description | 2017 July: Jalview and Dundee Resource Stand at ISMB/ECCB Conference in Prague, Czech Republic |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Jalview and the Dundee Resource were presented as a conference booth at ISMB/ECCB 2017 - the biggest annual conference in computational biology (attended by 2000 delegates). The booth was attended by the Jalview core development team and post-doctoral researchers working on the Dundee Resource, who demonstrated the capabilities of the resources and engaged with conference delegates about training, and the development of new features to help researchers and educators in their work. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.iscb.org/ismbeccb2017-exhibitors-sponsors/exhibitorlist |
| Description | 2017 June: One day workshop on Multiple Sequence Alignment with Jalview at The Australian National University |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Dr James Procter was invited by the Computational Biology and Bioinformatics Unit at The Australian National University to deliver a one day training course on the use of Jalview for multiple sequence alignment and analysis. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.jalview.org/training/training-courses/CBBU-Workshop-Multiple-Sequence-Alignment-with-Jalv... |
| Description | 2017 November - University of Dundee School of Life Scences Post Graduate Training Course on Protein Sequence Alignment and Analysis |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | A training course for life sciences post-graduates and post-doctoral researchers was delivered as a two workshops: The first was delivered by Dr James Procter and Dr Suzanne Duce and covered Multiple Sequence Alignment and Analysis with Jalview. The second workshop focused on Protein Sequence Analysis and Secondary Structure Prediction, and was delivered by Prof. Geoff Barton. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.jalview.org/training/training-courses/PhD-Postgrad-Sequence-Alignment-and-Analysis-Traini... |
| Description | 2018 January - Visit to Seaview Primary School to speak about Science, Proteins, and Jalview |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Dr Suzanne Duce was invited to give a talk on science, proteins and Jalview during a lesson at Seaview Primary School. In addition to physical demonstrations of how proteins fold, she also demonstrated how Jalview could be used to compare ancient human DNA to that of modern humans and show 3D molecular structures. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.jalview.org/Community/Community-news/Jalview-demonstration-at-Seaview-Primary-School |
| Description | 2018 Symposium Presentation: What can human variation tell us about proteins? University of Dundee Life Sciences Research Symposium (Creiff, Scotland) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Stuart MacGowan gave a short presentation on the analysis of human population genetic variation in Pfam domains. The presentation took place at the University of Dundee, College of Life Sciences Research Symposium during the postdoctoral and PhD student talk section. This symposium is attended by PIs, postdocs and PhD students from across the College of Life Sciences. |
| Year(s) Of Engagement Activity | 2018 |
| Description | 2019 July: Jalview and Dundee Resource Stand at ISMB/ECCB Conference in Basel, Switzerland |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Jalview and the Dundee Resource were presented as a conference booth at ISMB/ECCB 2019 - the biggest annual conference in computational biology (attended by 2000 delegates). The booth was attended by the Jalview core development team, and post-doctoral researchers and outreach officer working on the Dundee Resource, who demonstrated the capabilities of the resources and engaged with conference delegates about training, and the development of new features to help researchers and educators in their work. Our collaborator on the newly unveiled browser-based JalviewJS, Robert Hanson was also present at the meeting in order to showcase this new work. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.jalview.org/Conference/Conference-news/Jalview-at-ISMBECCB-2019-in-Basel |
| Description | 2019: Dec: School Visit to Forfar Academy, Angus by Dr B. Soares and Dr S. Duce to test newly released schools educational materials "Visualising DNA, RNA and Proteins in Jalview" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Ben Soares and Suzanne Duce tested the 'Visualising DNA, RNA & Proteins in Jalview' Schools Workbook with Dr Comrie's class of 17 Nat 5 biology pupils. A main objective of the visit was to evaluate the ease in which the practical activities in the lesson plan were accomplished by pupils in preparation for redesign of the lesson plan as a purely web-based activity with the JalviewJS web application. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.jalview.org/General/General-news/Jalview%E2%80%99s-Schools-Workbook-tested-by-pupils-at-... |
| Description | 2019: July: Jalview video screening as part of University of Dundee School of Life Sciences' Centre for Translational and Interdisciplinary Research showcase at UKRPIF output event London, UK |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | A one minute video was created by the Jalview and Dundee Resource Outreach Officer to explain the impact of the Jalview resource on UK research and education. The video was presented alongside other projects as part of a showcase highlighting the impact of the Centre for Translational and Interdisciplinary Research within the School of Life Sciences at the University of Dundee, which is an insitute made possible by investment from UKRPIF. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.youtube.com/watch?v=H14TeKaYEQ4 |
| Description | 2019: July: Talk by Dr S Duce at ISMB 2019 Education COSI in Basel, Switzerland: Crossing continents, experience of using video sharing services to deliver biological sequence analysis and visualisation training around the world |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr S Duce - the outreach officer for Jalview and the Dundee Resource was selected by the International Society of Computational Biology's Community of Special Interest (COSI) on Education to present at the 2019 ISMB Conference. The audience included educators and policymakers aiming to increase access to high quality educational materials and training in computational biology across the world and Dr Duce's talk described how Jalview's youtube videos, and its new browser based JalviewJS tool enab |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.iscb.org/cms_addon/conferences/ismbeccb2019/education.php |
| Description | 2019: Sep: Analysing dinosaur DNA with Jalview activities at Dundee Medical School's Doors Open Day, Ninewells Hospital, UK |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Dr Suzanne Duce provided hands on and digitial activities during a public open day event which enabled evaluation of materials being developed aimed at biological education in primary/secondary schools. |
| Year(s) Of Engagement Activity | 2019 |
| Description | 2020: June - Online Schools Outreach Event with Elgin Academy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Suzanne Duce had been invited up to Elgin Academy to run a Jalview Schools Workshop with the Higher and Advanced Higher Biology classes. This had to be cancelled due to the Covid-19 lockdown. Undeterred, the Jalview team ran the course remotely using Blackboard Collaborate. On Friday 12th June, Mungo Carstairs, Ben Soares and Suzanne Duce logged on and hosted the course with the students. We would like to thank Mrs Gordon of Elgin Academy and her staff for the invitation and their support. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.jalview.org/Community/Community-news/In-Covid-19-lockdown-the-Jalview-team-run-their-sch... |
| Description | 2020: March: Stall run by Dr. S. Duce at Dundee Women's Festival STEM Family Fun Day, Charleston Community Centre, Scotland, UK |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Jalview and the Dundee Resource's outreach officer ran a stall with hands on and digital activities including using JalviewJS to analyse DNA sequences extracted from samples from Tyranossaurus Rex fossils. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.jalview.org/General/General-news/Jalview-joins-the-STEM-Family-Fun-Day-at-Charleston-Com... |
| Description | 2020:July Dr Suzanne Duce Article in PDB's Education Corner: A Secondary School Bioinformatics Workbook for Visualizing DNA, RNA and Proteins |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Suzanne Duce, the outreach officer for Jalview and the Dundee Resource for Sequence Analysis and Structure Prediction was invited to write an article for the RCSPDB's News Letter about Jalview's schools outreach materials and events that she has lead the development of over the last 5 years in partnership with colleagues and UoD Masters students. It described how the materials were developed in order to enable younger learners to understand the relationship between DNA, RNA and Proteins, and how genetic variation can cause disease. This publication highlighted many of the free materials available on the Jalview web site that can be used by educators to develop computer based lessons or provided to pupils to work through on their own, and reported how JalviewJS - the web based version of Jalview, will improve accessibility of these materials. Web access statistics suggest the schools materials higlighted in the article were subsequently accessed over 600 times in September 2020 by users from over 80 countries. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://cdn.rcsb.org/rcsb-pdb/general_information/news_publications/newsletters/2020q3/corner.html |
| Description | 2020:Nov Dundee Science Festival Online Engagement: Exploring the double helix of DNA |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Dr Suzanne Duce compiled a selection of online videos and jalview schools materials presented as a web resource as part of the 2020 Dundee Science Festival's online program. The narrative introduced DNA and the central dogma with the help of animated videos, and why biologists need computational tools to investigate and analyse DNA, RNA and Protein, |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.dundeesciencefestival.org/2020-11-20-exploring-the-double-helix-of-dna |
| Description | BBSRC Eastbio DTP PhD workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | BBSRC Eastbio Doctoral Training Partnership PhD workshop for the students from St Andrews, Dundee, Edinburgh and Aberdeen University. "Jalview - Dundee born and bred software to interactively visualise, analyse and present your multiple sequence alignments" by Dr Suzanne Duce & Dr Jim Procter at 11:00 - 12:00 "Dataviz' in 30 mins: Do's, Don'ts, and where to learn more" by Dr Jim Proctor at 12:00 - 12:30 Jalview JS link Start Date: 27-02-2019 location: School of Life Sciences, University of Dundee Duration: 1 day |
| Year(s) Of Engagement Activity | 2018,2019 |
| URL | http://www.jalview.org/training/training-courses/BBSRC-Eastbio-DTP-PhD-workshop |
| Description | BI-LILLE (France) - Jalview workshop day |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited one-day Jalview workshop at BI-LILLE. Invitation was made after initial contact at Jalview exhibition booth at ISMB 2017 in Prague. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://wikis.univ-lille1.fr/bilille/jalview_2018 |
| Description | BI-LILLE (France) Invited talk: Integrating genomic variant data with RNA and Protein sequence, structure, function, and evolutionary analyses using the Jalview Desktop. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk on the latest developments in the Jalview platform for importing and filtering of VCF variant data from SNP call pipelines, given at Lille University. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.facebook.com/permalink.php?id=350436008397605&story_fbid=1710440752397117 |
| Description | Cell-ebration of Science on 3 May 2018. 105 primary school pupils from St Clement's and St Francis Primary Schools visited the School of Life Sciences |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Cell-ebration of Science on 3 May 2018. 105 primary school pupils from St Clement's and St Francis Primary Schools visited the School of Life. We ran hands on activity where pupils loaded the collagen protein sequence of Tyrannosaurus Rex from Uniprot database (P0C2W2) into Jalview. |
| Year(s) Of Engagement Activity | 2018 |
| Description | DRSASP Poster Presentation at Elixir-UK All Hands 2019 (Dundee) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Stuart MacGowan gave a poster presentation at the Elixir-UK All Hands 2019 meeting in Dundee. Some of the audience expressed interest in one or more of the tools within DRSASP whilst others were interested in the range of technologies employed and how we manage the maintenance of the resource. |
| Year(s) Of Engagement Activity | 2019 |
| Description | DRSASP Poster at Elixir-UK All Hands 2017 (Edinburgh) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Stuart MacGowan presented a poster overview of the DRSASP at the Elixir-UK All Hands 2017 (Edinburgh) meeting. Several meeting participants came to the poster to find out what the DRSASP was and the resources it provided. |
| Year(s) Of Engagement Activity | 2017 |
| Description | DRSASP Presentation at Elixir-UK All Hands 2019 (Dundee) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Stuart MacGowan presented an overview of the Dundee Resource for Sequence Analysis and Structure Prediction at the Elixir-UK All Hands 2019 meeting. The talk included a preview of the Slivka web services application and framework. This led to discussion around Slivka's potential relevance to several of Elixir's core objectives, especially improving the interoperability of bioinformatics tools and resources. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Dec 2016 Oxford: Seminar at WTCHG/SGC: Identification of novel functional sites in protein domains from the analysis of human variation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was an invited seminar at the Oxford SGC and WTCHG institutes in the Department of Medicine. The seminar described work that covered most of our funded research activities. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://talks.ox.ac.uk/talks/id/7b03765b-6d8a-45c0-bbb1-e570a70377ff/ |
| Description | Doors OpenDays |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | Yes |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Lots of questions from the public about what we do in Computational Biology. Also questions from potential future scientists (school children) about how computers are used in biology. Many discussions about different aspects of biological research and biomedical research in the media such as E.coli infection, ebola, cancer, diabetes, ageing and so on. We engage the public through a variety of open days and art/science projects. We had v. positive general feedback from the public about the interactions they had with us during each science festival. We heard that they were delighted by the opportunity to talk to the research leaders that worked in their local University. |
| Year(s) Of Engagement Activity | 2009,2010,2011,2012,2013,2014,2015,2016 |
| URL | http://www.dundeesciencefestival.org |
| Description | Feb 2017: Seattle: What can human variation tell us about protein structure? |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was an invited talk at the genevariation3d workshop at the Institute of Systems Biology which brought together scientists from the genomics/personalised medicine field and the field of protein structure analysis. I presented on our work at this interface that is built on Jalview and the Dundee Resource and inspired by our research in plant biology. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://genevariation3d.org/ |
| Description | Jalview and Dundee Resource - training videos 2017-present |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | YouTube Channel The Jalview YouTube channel has >312 subscribers and over 58K views. These are mostly training videos, although we have a few outreach videos. We made a short video about a student who was struggling with her assignment until she discovers one of our training workshop (708 views) https://youtu.be/uDUwQnaaU-o. Another video featured the Jalview team (1,818 views) https://youtu.be/KRt7xBtGYA0. We also have a video that we use at public outreach events (105 views) https://youtu.be/QvNNZeUku6g. |
| Year(s) Of Engagement Activity | 2017,2018,2019,2020 |
| URL | https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw |
| Description | Jalview and Dundee Resource Stand at ISMB/ECCB Conference 2015 Dublin |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We presented Jalview and the Dundee Resource at a conference booth for the three days of the ISMB2015 conference. This is the biggest annual international computational biology conference and allowed us to reach new audiences for our research and software tools as well as providing a base to forge new collaborations. Around 1500 people were at the conference and a large proportion of these visited the stand at some point in the conference. |
| Year(s) Of Engagement Activity | 2015 |
| URL | https://www.iscb.org/ismbeccb2015 |
| Description | Jalview and Dundee Resource Stand at the Microbiology Conference 2016, Liverpool, UK. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We presented Jalview and the Dundee Resource at a conference booth for the three days of the Microbiology Society conference. This allowed us to introduce a new group of users to Jalview and the Dundee Resources and also to re-engage with existing users. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.microbiologysociety.org/events/annual-conferences/index.cfm/annual-conference-2016 |
| Description | Mar 2017: Seminar at Newcastle University: Identification of novel functional sites in protein domains from the analysis of human variation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was an invited seminar to the Centre for Health and Bioinformatics at Newcastle University. I presented work at the interface between genomics/transcriptomics and protein structure which relied heavily on the software tools we develop and other resources. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.ncl.ac.uk/chabi/events/pastevents/item/eventgeoffbarton.html |
| Description | Multiple Sequence Alignment and Analysis: investigating structure and function of protein, RNA and DNA |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Date: 28th May, 2018 (from 9:30 to 16:00) Place: Cité Scientifique, Villeneuve d'Ascq BILILLE - Service en bio-informatique de Lille Instructor: James Procter (Jalview Coordinator, Division of Computational Biology, School of Life Sciences University of Dundee, UK) This hands-on workshop is for students and researchers working with Protein, RNA and DNA sequence data. Participants will learn how to create, analyse and visualise multiple alignments with the Jalview Desktop (www.jalview.org), and explore its capabilities for working with 3D structure, phylogenetic trees and annotation from public databases. Participants should bring their own laptop. Schedules 9.30am - Introduction to the Jalview Workshop 9.45am - Launching Jalview, importing, exporting and navigating alignments. 10.30am - Coffee break 11am - Creating multiple alignments 12.30pm - Lunch 1.30pm - Alignment analysis: Shading, Trees and Principal Component Analysis 2.30pm - Loading and Viewing 3D Structures 3pm - Working with Features and annotation tracks 3.30pm - Secondary structure and disorder prediction 3.55pm - Wrapup Registration Registration is free, but mandatory: form. The deadline is May 20th, 2018, and the number of participants is limited to 25. Organization Eva-Maria Krammer, Marc Lensink, Hélène Touzet (bilille@univ-lille.fr) Start Date: 28-05-2018 location: Université de Lille, France Duration: 1 day |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.jalview.org/training/training-courses/Multiple-Sequence-Alignment-and-Analysis-investigat... |
| Description | Multiple Sequence Alignment with Jalview and Protein Structure and Function Modelling |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Date: Monday 14th to Tuesday 15th May 2018 Time: 9.00 to 17.00 Location: MSTC, Sherrington Building, University of Liverpool, L69 3BX Overview This two day hands-on training course is aimed at students and researchers who want to gain practical understanding of the tools and approaches for protein sequence, structure and function prediction and analysis. In day 1, participants will be introduced to Jalview - a free desktop application for the visualisation and comparative analysis of protein, DNA and RNA sequences. Jalview can integrate data from Ensembl, Uniprot, PDBe, Rfam and Pfam, and can access a range of tools for multiple sequence alignment, conservation analysis and secondary structure and disorder prediction, including the widely used JPred4. On the second day, participants will learn to use Jalview's 3D structure visualisation capabilities in conjunction with UCSF Chimera, and take a whistle-stop tour of the methodologies and tools for prediction and analysis of Protein 3D structure and function. Participants are encouraged to bring their own protein analysis problems and time will be reserved at the end of day 2 for discussion. Please use this link to register: https://goo.gl/forms/wfq4oA2tficLErqV2 Day 1: Multiple Sequence Alignment and Analysis with Jalview Workshop trainers: Dr Jim Procter and Dr Suzanne Duce 9 9.15 Introduction to the Workshop 9.15 10.30 Session 1.Loading sequences, structures and alignments with Jalview Coffee break 11 12.30 Session 2. Multiple alignment Creation and Alignment Reliability Lunch 1.30 3pm Session 3. Phylogenetic trees and subfamily analysis of Proteins and CDS Coffee break 3.30 5pm Session 4. Protein secondary structure and disorder prediction, and working with annotation Day 2: Protein Structure Analysis and Modelling Workshop trainers: Dr Jim Procter and Dr Dan Rigden 9 9.15 Introduction to Workshop Day 2 9.15 9.30 Introduction to Protein 3D Structure 9.30 10 Viewing and Comparing 3D structures with Jalview and UCSF Chimera 10 10.30 Mapping sequence conservation to Biological Assemblies with Jalview Coffee Break 11 12.30 Functional analysis of Protein Structures Lunch 1.30 2.30 Homology modelling and model quality evaluation 2.30 3.15 Ab initio models and searching for fold matches 3.15 3.30 Wrap up: Function Analysis and 3D models Coffee Break 4pm 5pm Analyse your own protein sequences and structures. Course materials available at http://www.jalview.org/tutorial/training-materials/2018/Liverpool/ Start Date: 14-05-2018 to 15-05-2018 location: Sherrington Building, University of Liverpool, L69 3BX Links: Registration Workshop Poster Presentations Duration: 2 days |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.jalview.org/training/training-courses/Multiple-Sequence-Alignment-with-Jalview-and-Protei... |
| Description | Nov 2016 Rothamstead: Presentation to ELIXIR UK All Hands meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was a presentation on Jalview and the Dundee Resource to the ELIXIR-UK Group. The meeting followed on from the selection of our resources as Tier1 Elixir UK Resources. |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.elixir-uk.org/ |
| Description | PhD Induction Programme - Jalview Training |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Date: 27th & 28th September 2018 Location: Tower Building IT Suite D, University of Dundee Time: 13.00-17.00 on 27th September & 9.00-14.00 on 28th September Register: goo.gl/QpdqvX What is Jalview: Jalview is a versatile, free-to-use computer software developed at the University of Dundee. It is designed to assist research scientists visualise DNA, RNA and proteins. Jalview's multi-window interface allows you to view sequences, three-dimensional structures and trees. Sequences, structures and annotations can be load sequences directly from public biological databases. Course description: The course provides hands-on training in loading, editing, annotating and saving alignments, viewing 3D structure and implementing a range of analysis such as multiple sequence alignments. The course will involve presentations, hands-on exercises and demonstrations. Start Date: 27-09-2018 to 28-09-2018 location: Tower Building IT Suite D, University of Dundee Duration: 2 days |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.jalview.org/training/training-courses/PhD-Induction-Programme-Jalview-Training |
| Description | Presentation at 3DSIG-ISMB Prague |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Stuart MacGowan gave a presentation on the analysis of human population genetic variation in Pfam domains. The presentation was given to the 3DSIG COSI of ISMB Prague. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Presentation to Central South University, Changsha, China |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | I gave a talk about our recent research to a mixed audience of scientists and students at CSU, Changsha. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Presentation to the ELIXIR-UK All hands meeting at Birmingham University |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was an update to members of the ELIXIR-UK network and so helped to reinforce interactions within the network with other partners. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation to the Edinburgh Genomics meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was a scientific meeting focused on Genomics and included many people with a strong clinical research and application emphasis. My talk sparked interest in the new techniques we have developed that bring together human population genetics with protein structure and function. It also raised awareness of the Jalview and Dundee Resource systems that we develop with support from BBSRC and Wellcome Trust. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://biotexcel.com/event/genomic-medicine-2018-edinburgh/ |
| Description | Research seminar at the University of Kent |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I gave a presentation on our recent research on COVID-19 as well as new developments to Jalview and DRSASP. |
| Year(s) Of Engagement Activity | 2020 |
| Description | School of Life Sciences PhD Induction Online Programme 2020 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | A two day online workshop delivered over Blackboard Collaborate, consisting of hands-on exercises interspersed by short talks and Q&As. The first day introduced Jalview's features and functions. Participants learned how to load, save and export data, open the split screen viewer, and run the different analysis tools such as, sequence alignment, trees generation, principal component analysis, and viewing 3D structure. On the second day, participants gained experience using Jalview's web service capabilities for functional site analysis, secondary structure prediction and take advantage of its database clients to visualise genomic variation mapped onto protein 3D structure. |
| Year(s) Of Engagement Activity | 2020 |
| URL | http://www.jalview.org/training/training-courses/School-of-Life-Sciences-PhDMSc-Induction-2020 |
| Description | Seaview Primary School, Monifieth visit on 2nd February 2017. Suzanne Duce spoke to P7 class about science, proteins and Jalview (21 pupils). |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Seaview Primary School, Monifieth visit on 2nd February 2017. Suzanne Duce spoke to P7 class about science, proteins and Jalview (21 pupils). |
| Year(s) Of Engagement Activity | 2018 |
| Description | Seminar at Birkbeck, University of London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | This presentation focused on the analysis of human population genetics data and its link with protein structure and function. Examples were given that highlighted the use of our Jalview and Dundee Resource tools that are supported by BBSRC for the analysis. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Seminar at Garvan Institute, Sydney, Australia |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented recent research work to staff at the Garvan Institute and others in the region. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Seminar at Imperial College London |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | This was a presentation on recent developments with the Jalview visualisation and analysis system as well as basic research in the link between human population genetics and protein structure. |
| Year(s) Of Engagement Activity | 2017,2018 |
| Description | Seminar at Newcastle University, UK |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented recent research from my group to Research Group Leaders, Postdocs, Ph.D. Students, Undergraduates. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Seminar at Sydney University, Australia |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation about my group's research to the University of Sydney. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Seminar at Wellcome Trust Centre for Human Genetics, University of Oxford |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar describing wide range of research from my group. |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://talks.ox.ac.uk/talks/id/7b03765b-6d8a-45c0-bbb1-e570a70377ff/ |
| Description | Seminar to European Elixir All Hands Meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was a seminar about our Jalview and Dundee Resource activities funded by BBSRC and part of the ELIXIR-UK network. It brought other projects in the network up to date with our developments. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Seminar to Free Univesrity of Amsterdam, Netherlands |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented recent research from my group to Research Group Leaders, Postdocs, Ph.D. Students, Undergraduates. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Sept 2015: Invited Seminar at TGAC, Norwich |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented a broad range of our research at an invited seminar at The Genome Analysis Centre (TGAC) now, the Earlham Institute. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Variation in Proteins Poster at ISMB Prague 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Dr Stuart MacGowan presented a poster on the human variation in proteins research at ISMB Prague (2017) in the 3DSIG COSI. The poster followed his presentation and many audience members sought out the poster for further details and to ask more questions. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Variation in Proteins Presentation at NextGenBug 2017 (Dundee) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Dr Stuart MacGowan gave a presentation on our human variation in proteins research to the NextGenBug December 2017 (Dundee) meeting. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Viewing DNA, RNA and proteins with Jalview' Schools Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Schools |
| Results and Impact | On Thursday 12th April 2018, as part of Alssundgymnasiet Sønderborg School from Denmark visit to the School of Life Sciences. There is a wealth of biological data deposited in free, publicly accessible databases. However, the bioinformatics information is frequently located in several databases and often have their own specific file formats. To assist research scientist, a team at the University of Dundee have developed a fully integrated, multiple window desktop called Jalview to visualize and analyses sequences and three-dimensional structures of proteins, RNA and DNA. For example, Jalview can access public biological databases, perform multiple sequence alignments, construct trees, predict protein secondary structure, annotate sequences and overlay features such as active site residues. The hands-on workshop goals: To open Jalview from the 'Launch Jalview Desktop' link on the Jalview website and navigate the Jalview interface Fetch DNA and RNA sequences from public biological databases and colour the sequence bases Fetch myoglobin protein sequence from the UniProt database, colour the amino acid residues and view the 3D shape of the myoglobin View the myoglobin protein and the coding DNA (cDNA) in a split-screen window and identify the myoglobin exons Align the sequences using multiple alignment programs and generate a tree from the sequences Identifier List: DNA ID: adz17331 RNA ID: 2gis Protein ID: p02144 3D protein ID: 3rgk Alignment url: http://www.jalview.org/tutorial/myoglobins.mfa UniProt ID: P02144; P02147; P02185; P02192; P04247; P68276; P02197; P85077; P63113; P02190; P02187 Lanching Jalview Try this link: jnlp://www.jalview.org/webstart/jalview.jnlp or select and copy the text below into the clip board, and paste it into the Windows start menu, then press return ! (Press the windows button to open the start menu). javaws http://www.jalview.org/webstart/jalview.jnlp Remember to make sure the checkbox for 'Trust this publisher' is UNTICKED ! (this is a problem with our system here in Dundee). Start Date: 12-04-2018 location: 1G01 ITSuite 1 room, Dalhousie, University of Dundee Duration: 2 hours |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.jalview.org/training/training-courses/Viewing-DNA-RNA-and-proteins-with-Jalview-Schools-W... |