Integrative Biology
Lead Research Organisation:
THE PIRBRIGHT INSTITUTE
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
Modern high-throughput techniques (DNA/RNA-sequencing, ChIP-sequencing, ribosome profiling, mass-spectrometry) and subsequent high-performance bioinformatics data analysis have revolutionized the way we understand biology. The Integrative Biology project at the Pirbright Institute aims to put together in a problem-dependent way a number of such techniques, in order to precisely interrogate at each time point a set of compartments of the cell and hence gain a better overall understanding of its inner workings during the whole duration of the biological process. System studied will be the animal virology ones found at Pirbright. In fact, thanks to the extraordinary mechanisms of action of viruses such systems offer a privileged probing window into the operation of the basic mechanisms of the cell; at the same time, the usage of animal models allows for a direct testing of scientific hypotheses in vivo. In order to set up protocols suitable for the high-precision study of the main biological systems available at Pirbright, the project will be constantly exchanging knowledge and expertise with all the many relevant groups existing both inside and outside the institute.
Planned Impact
unavailable
Publications
Abascal F
(2016)
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.
in Genome biology
Abolins-Abols M
(2018)
Differential gene regulation underlies variation in melanic plumage coloration in the dark-eyed junco (Junco hyemalis).
in Molecular ecology
Alioto TS
(2015)
A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.
in Nature communications
Chacón A
(2015)
Boosting the FM-Index on the GPU: Effective Techniques to Mitigate Random Memory Access.
in IEEE/ACM transactions on computational biology and bioinformatics
Cruz F
(2016)
Genome sequence of the olive tree, Olea europaea.
in GigaScience
Fereidouni S
(2019)
Mass Die-Off of Saiga Antelopes, Kazakhstan, 2015.
in Emerging infectious diseases
Ferretti L
(2018)
Within-Host Recombination in the Foot-and-Mouth Disease Virus Genome.
in Viruses
| Description | This award (which is the core funding for the Integrative Biology and Bioinformatics group at Pirbright) has been instrumental to setting up a centralised bioinformatics and sequencing group which is now an essential hub of scientific activity at Pirbright. During the reporting period we have put in place and administered a high-performance computing platform for the whole institute, together with a full complement of analysis workflows; and more recently, having secured an ad-hoc award of >0.5M£, we have greatly expanded the sequencing unit within the National Capability SAPO4 high-containment lab at Pirbright. Thanks to our effort, Pirbright now has cutting-edge integrated sequencing-in-containment and bioinformatics data analysis capabilities; they can be used to produce outstanding science, and will be central to the goals of the next funding cycle. The award generated a relevant amount of additional funding coming from a variety of sources. Starting with the reporting period we have also devised several novel data analysis methods optimised for virology (notably a sensitive assembly pipeline and SNP caller, plus several integrative workflows) which are becoming the tool of choice at Pirbright; we have secured scientific collaborations with most of the groups at the Institute and some groups abroad; and we have started the production of scientific data for specific projects, both as a group and in collaborations. For instance we have helped identifying sex-specific genes in A.gambiae; helped characterising some sub-populations of bovine B cells from their transcriptional profile; and demonstrated the existence of widespread recombination in the FMDV capsid in African buffaloes. We have created bioinformatics resources to allow and democratise access to data generated at the Institute on relevant livestock diseases - notably the FMDV Toolkit for the FMDV World Reference Lab, and the upcoming Portal for Transboundary Pathogens funded by BBSRC under a GCRF call. |
| Exploitation Route | Our work will be essential for all the groups at Pirbright using sequencing and bioinformatics as tools for their exploration of biological systems. In the case of some of the bioinformatics resources we have generated (notably the FMDV Toolkit website, and the upcoming Portal for Transboundary Pathogens) they will be relevant to policy making, especially in low- and middle-income countries. |
| Sectors | Agriculture Food and Drink Government Democracy and Justice Security and Diplomacy |
| Description | 1. Our group has been supplying state-of-the-art bioinformatics tools to the World Reference Labs for the Foot-and-Mouth Disease Virus. The tools are based upon a database of genomic sequences and metadata for FMDV samples. Some tools allow members of the lab to enter, process and annotate new data into the database, generating several kinds of reports that are used to inform FMDV policy-makers both within the UK and in the rest of the world. Other web-based tools allow external users to query the database in various ways, the focus having been placed on scientists from LMI countries. 2. The award holder has been conducting research on data compression, is actively involved in the design of the upcoming MPEG-G standard for the compression of genomic information, and is now an accredited member of the British Standards Institution (BSI). A novel standard for the compression of genomic data would help tackling the current deluge of sequencing data, which is placing a big infrastructural burden on all consumers of sequencing technologies. The standard plans to address most of the shortcomings of current solutions (notably the lack of format flexibility and the suboptimal compression level) and would presumably be of the utmost interest to all the actors playing in the field of sequencing. |
| Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Government, Democracy and Justice,Manufacturing, including Industrial Biotechology,Security and Diplomacy |
| Impact Types | Economic Policy & public services |
| Description | Membership of MPEG-G (standardisation of the compression of genomic information) working group |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Membership of a guideline committee |
| Description | Organised seminar series on Sequencing, Virus Evolution and Molecular Biology at Pirbright (with Luca Ferretti and Graham Freimanis) |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Description | Taught bioinformatics (sequence analysis) to Oxford Biosciences DTC and Murcia Bioinformatics Master |
| Geographic Reach | Europe |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Description | Taught course on introductory bioinformatics to PhD students at Pirbright |
| Geographic Reach | Local/Municipal/Regional |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Description | (CloudButton) - Serverless Data Analytics Platform |
| Amount | € 4,277,507 (EUR) |
| Funding ID | 825184 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 01/2019 |
| End | 12/2021 |
| Description | ARBONET |
| Amount | £63,887 (GBP) |
| Funding ID | BB/N023889/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2016 |
| End | 02/2019 |
| Description | BBSRC Responsive Mode |
| Amount | £630,378 (GBP) |
| Funding ID | BB/P019269/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 05/2020 |
| Description | BBSRC Responsive Mode |
| Amount | £522,923 (GBP) |
| Funding ID | BB/P019137/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 05/2020 |
| Description | Capital/infrastructure bid |
| Amount | £552,000 (GBP) |
| Funding ID | Capital bid for sequencing equipment in the Pirbright National Capability SAPO4 laboratory |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2018 |
| End | 04/2018 |
| Description | Horizon2020 |
| Amount | € 1,900,000 (EUR) |
| Funding ID | DEFEND |
| Organisation | European Union |
| Sector | Public |
| Country | European Union (EU) |
| Start | 04/2018 |
| End | 04/2022 |
| Description | International partnering awards - Taiwan-UK Partnering Awards |
| Amount | £15,400 (GBP) |
| Funding ID | BB/R02121X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2020 |
| Description | Newton Fund - UK-China partnership on Global Food Security |
| Amount | £389,043 (GBP) |
| Funding ID | BB/R012865/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2018 |
| End | 12/2020 |
| Description | Responsive mode |
| Amount | £605,275 (GBP) |
| Funding ID | BB/R008833/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2018 |
| End | 01/2021 |
| Description | Safe Genes |
| Amount | $4,882,699 (USD) |
| Organisation | Defense Advanced Research Projects Agency (DARPA) |
| Sector | Public |
| Country | United States |
| Start | 03/2017 |
| End | 03/2022 |
| Title | Method for sequencing of ASFV (African Swine Fever Virus) based on long reads |
| Description | The ASFV genome is repetitive, due to the presence of families of genes that are present in multiple copies (>10). As a result, sequencing based on short reads only would not be able to reconstruct the genome in its entirety. In addition, good quality full genome sequencing of ASFV is complicated by persistence contamination with fragments of host DNA. We are developing a novel protocol that will allow the sequencing of the virus using long-read technologies (PacBio or Oxford Nanopore). Probe-capture libraries have been designed to mitigate the problem of host contamination by selectively purifying viral DNA from a wide range of different ASFV genotypes. Protocols are being developed to prepare high quality high molecular weight viral DNA from different sample types suitable for generating sequencing libraries for long-read sequencing. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | More than 100 samples from 18 different LMIC countries have been identified and collated for sequencing with the new protocol. They will be added to the web-portal for transboundary pathogens which is currently being developed thanks to BBSRC funding. |
| Title | Method to evenly load flowcells with multiple samples |
| Description | Pirbright has an Illumina NextSeq sequencing machine installed in containment. Given the large amount of sequencing reads produced by each run, multiple samples are usually multiplexed on the same flowcell. However, determining the correct concentrations needed to obtain the same amount of reads for each sample is a hard problem, and usually requires a number of expensive and material-consuming kits to be run prior to sequencing. We have developed a method that allows samples to be evenly multiplexed based only on Bioanalyzer data (we routinely run Bioanalyser on the samples anyway as a form of quality control). The method works well, and reliably across a wide range of sample concentrations and sequenced organisms. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | The method greatly increased the quality of our output, and drastically simplified our workflow by eliminating the external quantification steps that were previously required. |
| Title | Boosting the FM-index on the GPU |
| Description | The FM-index is a data structure that lies at the core of most modern short-read aligners. Our work describes what is perhaps the first implementation of the FM-index on the GPU able to take full advantage of the high hardware parallelism (large number of computing cores) offered by modern Graphical Processing Units. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2016 |
| Provided To Others? | No |
| Impact | Short-read aligners are instrumental to the analysis of high-throughput sequencing experiments. As alignment is central to most analysis pipelines, speeding it up is essential to improve the performance of many bioinformatics tools. Thanks to our new algorithm FM-index based searches can be sped up by a large factor on all computers where a suitable GPU is present. |
| Title | FMDV LIMS and webtools |
| Description | The Integrative Biology and Bioinformatics (IBB) group has been supplying state-of-the-art bioinformatics tools to the World Reference Labs for the Foot-and-Mouth Disease Virus. All tools revolve around a database of genomic sequences and metadata for FMDV samples. Some tools allow members of the lab to enter, process and annotate new data into the database, generating several kinds of reports. Other web-based tools (the "FMDV Toolbox") allow external users to query the database in several ways. Bioinformatics workflows are hosted on the IBB cluster, and have been implemented as REST web services so as to be decoupled from the web interface. The web interface is currently being redeveloped with the help of a specialised company. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | The reports generated by our system are used to inform FMDV policy-makers both within the UK and in the rest of the world. External users can compare their sequences to those contained in the database, and get useful biological insights. |
| URL | https://mallorn.pirbright.ac.uk/FMDVToolbox |
| Title | GCRF portal on transboudary diseases |
| Description | The Integrative Biology and Bioinformatics group is developing a GCRF-funded Portal on Transboundary Diseases. It will be an easy way for all scientists, and those from LMI countries in particular, to access data about several viral diseases generated at Pirbright. The portal will be country-based, presenting the user with a map and dispatching them to the information relevant to the selected region. From that information the user will be able to reach specialised websites for diseases present in the country, and data generated at Pirbright (such as sequences for FMDV, several Capripox viruses, and ASFV). Sequences relevant to the portal are currently being generated. Bioinformatics workflows are hosted on the IBB cluster, and have been implemented as REST web services so as to be decoupled from the web interface. The web interface is currently being developed with the help of a specialised company. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | The portal will benefit scientists from LMI countries, and all scientist, allowing them to access/download genetic and other data relevant to animal diseases present in a country of choice and studied and Pirbright. Some of the data (for instance the FMDV data generated by the World Reference Lab) is already use to inform policy at international level. Being able to access information in a systematic way will increase the potential for it to be put to good use. |
| Title | Genome browser for MDV infected chicken cells |
| Description | The database integrates and makes available the results of the bioinformatics analysis of several experiments involving high-throughput sequencing of chicken cells infected by several viruses (mainly Marek's Disease Virus) generated within the Avian Viral Disease group at the Pirbright Institute. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | The genome browser allows the researchers to meaningfully mine and integrate the large amount of data produced by their experiments, guiding subsequent experimental hypothesis-driven validation in the lab. |
| Title | Genome browser for mosquitos at different developmental stages |
| Description | The database integrates and makes available the results of the bioinformatics analysis of several experiments involving high-throughput sequencing of mosquito cells at different developmental stages generated within the Vector-borne Viral Disease group at the Pirbright Institute. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | The genome browser allows the researchers to meaningfully mine and integrate the large amount of data produced by their experiments, guiding subsequent experimental hypothesis-driven validation in the lab. |
| Title | Method to detect the expression of repetitive genes |
| Description | Reconstructing expression levels of genes having a high repeat content is difficult, due to the impossibility of assigning RNA-sequencing that have multiple mappings to their correct originating location. In collaboration with the Immunogenetics group, the Integrative Biology and Bioinformatics groups are developing a data analysis method to circumvent the problem.The method has already been shown to be effective on some KIR genes in cattle. An essential component of the immune system, their family is rich in repeated members and repetitive regions, making the technique essential if one wants to study them. |
| Type Of Material | Data analysis technique |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | Being able to resolve the expression of repetitive genes, which are plentiful in most mammalian genomes, would be essential to the high-precision study of many important gene families, including most of the genes of the immune system. The technique has already proven itself effective on a real-life problem, and holds the potential to be extended to many more biological systems |
| Title | Method to predict vaccine matching in-silico |
| Description | Every time a novel viral strain emerges, it is essential to know whether existing vaccines are effective against it. Several lab techniques are available in order to do so, the most widespread one arguably being VNT (virus neutralisation test). However VNT is expensive, difficult to implement and not very reproducible due to batch effects. Being able to reliably predict VNT-derived antibody titres with the computer would be a game changer in the field. We have developed an in-silico model based on machine learning that is able to effectively predict VNT outcomes out of sequencing data. We have shown that the method performs well for FMDV and also, apparently, for influenza. |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | We are currently in the process of validating and optimising the method. If preliminary results are confirmed, the method could be put to good use in a number of fields, and become the basis for a more effective policy making when managing and controlling devastating livestock diseases such as FMDV. |
| Title | South-African buffalo FMDV sequences |
| Description | We have sequenced FMDV buffalo samples originated from a EEID project entitled: Persistence of a Highly Contagious Pathogen: Ecological and Evolutionary Mechanisms in Foot-And-Mouth Disease Virus. This project aims to understand why a highly contagious pathogen such as FMDV, which induces a rapid host immunity and depletes the supply of susceptible host, is able to persist in isolated buffalo populations and thus avoid auto-extinction. The centre piece of the project is a cohort study which involves an established FMDV-positive breeding herd of ca. 70 buffalo in a 900-hectare enclosure surrounded by double game fencing housing buffalo in isolation from other herds in the Kruger National Park (South Africa). The entire herd is being monitored for three years (animals are sampled every 2 months (serum, tonsil swabs, probang) to trace FMDV transmission events, allowing us to define FMD infection dynamics across the susceptible calf cohorts and amongst adults. So far, FMDV genomes from 101 samples have been deep sequenced by illumina. Samples from the last year captures are currently being analysed and virus is currently being isolated. The second experiment is an experimental study, which involves a group of naïve buffalo experimentally infected with either a SAT-1, SAT-2 or SAT-3 virus. The infected buffalo were then allowed to mingle with susceptible animals and transmission of FMDV to naïve animals was monitored during the acute infection but also from persistently infected animals. So far, FMDV genomes from 48 samples obtained at days 2, 30 and 160 of the experiment have been deep sequenced. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | The samples sequenced come from South Africa, which is an LMIC, While FMDV infection in cattle is very well studied, the mechanisms of persistence in buffalo, which is thought to be the natural reservoir of the infection, are not well understood. Such understanding would be essential to inform better policies to understand and manage FMDV, which is an economically important scourge of cloven hooved animals in LMICs. All the sequences will be made available on the Transboundary Portal which is being developed at Pirbright. |
| Title | Viral assembly pipeline |
| Description | The Integrative Biology and Bioinformatics group has developed a data analysis pipeline to obtain sensitive and robust viral assemblies out of high-throughput sequencing data. In spite of the relatively short genomic length of most viruses, assembling of viral sequences can be challenging due to several reasons, such as: low amount of material in the sample, which might require amplification, introducing biases, and/or generates low-quality sequences; uneven coverage due to low-quality material or the genomic material of the virus being RNA; the viral nucleic acid being almost lost in the background of nucleic acid of the host. Our pipeline overcomes most of those problems, and is even able to detect different viral strains being present together in the same sample. It can also be used on metagenomic environmental samples. |
| Type Of Material | Data analysis technique |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | The pipeline is being deployed as the tool of choice for the nascent sequencing facility at Pirbright. It has been used by several groups at Pirbright, and the FMDV World Reference Lab, in order to assemble very different kinds of viruses. |
| Title | Viral variant calling pipeline |
| Description | The Integrative Biology and Bioinformatics group has developed a data analysis pipeline to obtain sensitive and robust variant calling for viral sequences out of high-throughput sequencing data. In spite of the relatively short genomic length of most viruses, calling variant for viral sequences can be challenging due to several reasons, such as: low amount of material in the sample, which might require amplification, introducing biases, and/or generates low-quality sequences; very high genome coverage, which slows down most existing variant callers; the presence of a potentially very high number of different haplotypes for RNA viruses, which is an unusual scenario in variant calling. Our fast and sensitive Bayesian pipeline overcomes most of those problems. |
| Type Of Material | Data analysis technique |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | The pipeline is being deployed as the tool of choice for the nascent sequencing facility at Pirbright. It has been used by several groups at Pirbright, and the FMDV World Reference Lab, in order to assemble very different kinds of viruses. |
| Title | WRL FMDV sequences for transboundary portal |
| Description | We have generated a collection of sequences of FMDV (foot-and-mouth disease virus) from samples collected by the FMDV World Reference Laboratory at Pirbright. Those full-genome sequences sample a number of recent exotic strains across different regions/countries of the world, focusing mainly on LMICs in North Africa, Middle East and South East Asia. The main represented FMDV types are O and A. Part of the sequences have already been made available through GenBank -- all will be soon downloadable from the Transboundary Portal which is being developed at Pirbright. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Knowledge of the sequenced strains is essential to inform policy for FMDV control in the LMIC countries where the samples were collected. That chimes very well with the GCRF focus of the project. At a more global scale, knowledge of the features and sequence evolution of the virus in time and across different countries is essential in order to accurately model its behaviour. In general FMDV is a scourge of cloven-hoofed animals, and controlling it better is essential in order to alleviate the huge economic toll claimed by the virus in LMICs. |
| Title | Zimbabwe FMDV sequences |
| Description | Foot-and-mouth disease virus (FMDV) causes an acute vesicular disease in domestic cloven-hooved animals. However, in the African buffalo (Syncerus caffer) clinical disease is rarely observed and following infection virus is persistently carried in the oesophageal-pharyngeal area of the upper respiratory tract. During the 1990s oesophageal-pharyngeal scrapings were collected from free-living African buffalo in multiple herds in six different geographic areas of Zimbabwe. We sequenced over 140 FMD viruses each belonging to one of the Southern African Territories (SAT) serotypes (SAT 1, SAT 2 and SAT 3) from primary bovine thyroid cells. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | This dataset has been generated from samples collected in Zimbabwe, which is a low-income country. Those viral sequences will be essential to help elucidating the nature of persistent FMDV infection in African buffalo, which is supposed to be the main virus reservoir in vivo. As the samples track viral infection and evolution over several years and across a number of different herds in different national parks and conservatories, the dataset will also inform better animal management and conservation. A better understanding of FMDV persistence would also be essential to mitigate the economic burden generated by the disease, which is a scourge of cloven-hoofed animals in LMICs. All the sequences will be made available through the Transboundary Pathogen portal that is being developed at Pirbright. |
| Description | Anopheles reannotation |
| Organisation | Centre for Genomic Regulation (CRG) |
| Country | Spain |
| Sector | Academic/University |
| PI Contribution | Provided RNA-sequencing data (produced by Jaroslaw Krzywinski and analysed by us) |
| Collaborator Contribution | Using the data to produce a reannotation of Anopheles Gambiae |
| Impact | No outputs yet |
| Start Year | 2017 |
| Description | Re-annotation of Marek's Disease Virus |
| Organisation | U.S. Department of Agriculture USDA |
| Department | Beltsville Agricultural Research Center |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | We are using bioinformatics analysis of high-throughput sequencing data in order to provide a better annotation of the genome of Marek's Disease Virus |
| Collaborator Contribution | Our partners are sharing their extensive expertise of the genomics of MDV, and performing experimental validations |
| Impact | No output yet |
| Start Year | 2015 |
| Description | Semliki Forest |
| Organisation | The Pirbright Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Generated and analysed RNA-sequencing samples with bespoke in-house methods |
| Collaborator Contribution | Generated samples |
| Impact | The purpose of the collaboration is to study how arboviruses interact with their host cells with modern high-throughput techniques. No outputs yet |
| Start Year | 2017 |
| Description | Vaccinia |
| Organisation | Defence Science & Technology Laboratory (DSTL) |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Generated and analysed DNA- and RNA-sequencing data from vaccinia samples with bespoke in-house pipelines |
| Collaborator Contribution | Generated DNA and RNA vaccinia samples |
| Impact | The collaboration aims to better understand the interaction between vaccina virus and its host(s), through the use of modern high-throughput techniques. No outputs yet |
| Start Year | 2016 |
| Title | CARGO: effective format-free compressed storage of genomic information |
| Description | CARGO is a compressor compiler. Given a high-level description of a file format (such as FASTQ or SAM) and compression methods for each field, it automatically generates optimized (de)compressors for such a format. Random access and range queries are provided for sorted datasets. Arbitrary sets of CARGO-compressed files can be stored together in a CARGO container. |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Impact | Technical solutions derived from CARGO are being discussed for incorporation into the upcoming MPEG (Moving Picture Experts Group) standard for the compression of genomic information |
| Description | Bull/Intel press release |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | The Integrative Biology and Bioinformatics group at Pirbright has acquired a bespoke computer cluster for genomics from Atos/Bull. Paolo Ribeca and Bryan Charleston were asked by Atos/Bull and Intel to contribute to a case study that illustrates the usefulness of high-performance computing in combating animal diseases and improving livestock welfare. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://globenewswire.com/news-release/2017/01/10/904852/0/en/The-Pirbright-Institute-chooses-an-Atos... |
| Description | Career fair (Bishop David Brown School) |
| 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 | Hundreds of pupils attended the school fair and discussed the role of the Pirbright Institute and related career options. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Career fair (Gordon School) |
| 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 | A few hundred pupils attended the fair and about a hundred of them visited our stand and interacted with us to understand better our work and the future career perspectives. Many students interested in related careers. |
| Year(s) Of Engagement Activity | 2016,2017 |
| Description | EUFMD 2016 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | During the EuFMDV conference taking place from 26 to 28 October 2016, Paolo Ribeca gave a talk on "VIBAsys and FMDV-Tools: Practical resources for FMDV sequence analysis". The conference, organised by the EU, gathers most of the important actors in FMD control. The talk explained how the new resources being developed by the Integrative Biology and Bioinformatics on behalf of the FMDV World Reference Lab can be useful to the community |
| Year(s) Of Engagement Activity | 2016 |
| Description | GFRA meeting in Incheon, South Korea |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at the meeting of the Global FMD Research Alliance, sparking a discussion on the role of multiple infections and recombination on the evolution of the disease. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.cvent.com/events/2017-gfra-scientific-meeting-seoul-korea/event-summary-53b3dd0f843245e08... |
| Description | Invited member of the Program Committee of AlCoB (Algorithms for Computational Biology) 2016 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I was invited to join the Program Committee of the Algorithms for Computational Biology conference 2016 |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://grammars.grlmc.com/AlCoB2016/pc.php |
| Description | Invited member of the Program Committee of AlCoB (Algorithms for Computational Biology) 2018 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I was invited to join the Program Committee of the Algorithms for Computational Biology conference 2018 |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://grammars.grlmc.com/AlCoB2018/pc.php |
| Description | Invited member of the Program Committee of ECCB (European Conference on Computational Biology) 2016 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | I was invited to join the Program Committee of the European Conference on Computational Biology 2016 |
| Year(s) Of Engagement Activity | 2016 |
| URL | https://www.ebi.ac.uk/eccb/2016/home/committees-2/index.html |
| Description | MDV conference Tours 2016 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | During the 11th International Symposium on Marek's Disease and Avian Herpesviruses, which took place from 6 to 9 July 2016, Paolo Ribeca gave a talk on "Attenuation of MDV: an RNA-seq based perspective". |
| Year(s) Of Engagement Activity | 2016 |
| Description | MPEG-G working group at Pirbright |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | From 27 to 29 September 2017 Paolo Ribeca organised and hosted at Pirbright an ad-hoc meeting of the MPEG working group on genome compression (MPEG-G). The meeting focused on writing and improving technical documents needed to establish the upcoming standard. Many aspects of generation, use, storage and retrieval of genomic information were discussed during the meeting, as well as technical details of compression algorithms suitable for high-throughput sequencing data. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Paolo's talk on FMDV vaccine matching |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Paolo Ribeca gave a talk at the 2018 Open Session of EuFMD (European commission for the control of foot-and-mouth disease ) on "Effective in-silico sequence-based prediction of FMDV vaccine matching" on behalf of Yasaman Kalantar-Motamedi, Mana Mahapatra, Luca Ferretti, Sophie Mahendran, Satya Parida, and himself. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster by Nick on the sequencing of Zimbabwe FMDV |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Nick Knowles presented a poster at the 2018 Europic (the meeting of the European Study Group on the Molecular Biology of Picornaviruses) on "Complete Genome Sequence Analysis of Over 140 Foot-and-mouth Disease Viruses Isolated From Free-living African Buffalo (Syncerus Caffer) in Zimbabwe" on behalf of Jemma Wadsworth, Bruce Bolt, Luca Ferretti, Euan C. Anderson, Ashley Gray, Paolo Ribeca, and himself. The sequencing was funded by the Transboundary Pathogens portal project awarded to Pirbright. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Talk by Nick on the sequencing of Zimbabwe FMDV |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Nick Knowles gave a talk at the 2018 Open Session of EuFMD (European commission for the control of foot-and-mouth disease ) on "Complete Genome Sequence Analysis of Over 140 Foot-and-mouth Disease Viruses Isolated From Free-living African Buffalo (Syncerus Caffer) in Zimbabwe" on behalf of Jemma Wadsworth, Bruce Bolt, Luca Ferretti, Euan C. Anderson, Ashley Gray, Paolo Ribeca, and himself. The sequencing was funded by the Transboundary Pathogens portal project awarded to Pirbright. |
| Year(s) Of Engagement Activity | 2018 |
| Description | UK-India bioinformatics workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | On February 9 2018 Pirbright organised a "UK-India bioinformatics workshop" in order to foster ties between Indian and UK bioinformaticians working in the field of livestock and crop research. Paolo Ribeca gave a talk on "Bioinformatics and sequencing at Pirbright". |
| Year(s) Of Engagement Activity | 2018 |