Quadram Institute Bioscience UKRI Innovation Fellowships: BBSRC Flexible Talent Mobility Accounts
Lead Research Organisation:
Quadram Institute Bioscience
Department Name: Directorate
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.
People |
ORCID iD |
| Reg Wilson (Principal Investigator) |
Publications
Birolo G
(2020)
covtobed: a simple and fast tool to extract coverage tracks from BAM files
in Journal of Open Source Software
| Description | Sustained Energy Release Starchy Food Products |
| Amount | € 659,474 (EUR) |
| Funding ID | 20169 |
| Organisation | European Institute of Innovation and Technology (EIT) |
| Sector | Public |
| Country | Hungary |
| Start | 01/2020 |
| End | 12/2021 |
| Title | Equipment for gut-on-chip |
| Description | Gut-on-chip system is run by specialised equipment consisting of two parts: Zoe and Orb. Zoe controls the rate of flow and peristalsis-like stretch for up to 12 chips, providing the environment cells need to live. Orb provides the precise mixture of gas, power, and vacuum stretch required by the Zoë culture module. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Following initial experiments with gut-on-chip and demonstrating exciting results using this dynamic microfluidics system (as opposed to the conventional static methods such as trans wells) we were able to attract funding by an industrial collaborator for a pilot study using this state of the art method. |
| URL | https://www.emulatebio.com/products |
| Title | Gut-on-chip technology established |
| Description | Gut-On-Chip microfluidic culture device recapitulates the microarchitecture and functions of living intestine. Using the organoid approach where intestinal stem cells isolated from human biopsies are processed to form intestinal villi oriented towards the channel lumen, and the epithelium in close apposition to human intestinal microvascular endothelium. This Gut-on-Chip GOC technology using donor-derived human intestinal cells therefore offers advantages over the current organoids and creates new opportunities for personalized medicine including the transport of nutrients, digestion, different intestinal disorders, and intestinal interactions with commensal microbes as well as pathogens. |
| Type Of Material | Model of mechanisms or symptoms - in vitro |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Following initial experiments with gut-on-chip and demonstrating exciting results using this dynamic microfluidics system (as opposed to the conventional static methods such as trans wells) we were able to attract funding by an industrial collaborator for a pilot study using this state of the art method. |
| URL | https://www.nature.com/articles/s41598-018-21201-7 |
| Description | UniPD_UniVR |
| Organisation | University of Padova |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | - Our team introduced the use of NextFlow workflows for reproducible pipelines and how to package software in BioConda to allow for easy installation/distribution; - I delivered a research seminar at the University of Padua and a science dissemination talk for high-school students; - Hosted at UniPD for 10 days to collaborate on metagenomics methods |
| Collaborator Contribution | - Prof. Chiara Romualdi organized and delivered a training session on "statistical methods for RNA-Seq analysis" - Prof. Nicola Vitulo organized and delivered a training session on "Interpreting data from metabarcoding experiments" |
| Impact | - one-to-one session with Prof. Chiara Romualdi, statistician, resulted in improved statistical methods implemented in our microbiome statistical analysis; - collaborating with Prof. Nicola Vitulo, bioinformatician, we developed a pipeline for virome analysis that will be presented at the RECOMB2020 conference in May 2020. |
| Start Year | 2019 |
| Description | UniPD_UniVR |
| Organisation | University of Verona |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | - Our team introduced the use of NextFlow workflows for reproducible pipelines and how to package software in BioConda to allow for easy installation/distribution; - I delivered a research seminar at the University of Padua and a science dissemination talk for high-school students; - Hosted at UniPD for 10 days to collaborate on metagenomics methods |
| Collaborator Contribution | - Prof. Chiara Romualdi organized and delivered a training session on "statistical methods for RNA-Seq analysis" - Prof. Nicola Vitulo organized and delivered a training session on "Interpreting data from metabarcoding experiments" |
| Impact | - one-to-one session with Prof. Chiara Romualdi, statistician, resulted in improved statistical methods implemented in our microbiome statistical analysis; - collaborating with Prof. Nicola Vitulo, bioinformatician, we developed a pipeline for virome analysis that will be presented at the RECOMB2020 conference in May 2020. |
| Start Year | 2019 |
| Description | UniTO |
| Organisation | University of Turin |
| Country | Italy |
| Sector | Academic/University |
| PI Contribution | - I introduced technical aspects on software engineering to Dr. Giovanni Birolo and Dr. Serena Aneli: Docker containers, packaging and distribution of software using BioConda, unit tests and continuous integration using Circle-CI; - Joint development of a novel tool for analysis of next generation sequencing alignments - Joint development of a novel tool for denoising of OTU table in 16S sequencing experiments |
| Collaborator Contribution | - Dr. Serena Aneli delivered a seminar - Dr. Giovanni Birolo worked on a bioinformatics project at the Quadram Institute for one week, coding software (CovToBed and OTUSfocus)- - Dr. Giovanni Birolo delivered training on "Python - Pandas" |
| Impact | - A publication describing "covtobed" has been submitted - The software "covtobed" has been released open-source, distributed on BioConda (> 1000 downloads) and Docker Hub. - A manuscript describing the OTU table cleaning tool is under preparation |
| Start Year | 2019 |
| Title | Galru: rapid pathogen typing using CRISPR spacer repertoire |
| Description | Galru is a Python 3 program that defines CRISPR spacer repertoire directly from uncorrected metagenomic long reads. Galru first identifies long reads that map to CRISPR-associated genes and searches along the read for the CRISPR spacer array. This array is compared to a database of known arrays to identify the sequence type (MLST). |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | None yet |
| URL | https://github.com/quadram-institute-bioscience/galru |
| Title | Singularity image of "covtobed" - a tool to convert coverage tracks to BED files |
| Description | Covtobed 1.0RC Read one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. https://github.com/telatin/covtobed/ |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | The singularity image allows to execute the software in HPC environments avoiding installation of libraries and dependencies. This image has been installed in the Norwich Research Park High Performance Cluster. |
| URL | https://zenodo.org/record/3600261 |
| Title | covtobed - a new tool to extract coverage information |
| Description | covtobed is a tool to generate BED coverage tracks from BAM files, that reads one (or more) alignment files (sorted BAM) and prints a BED with the coverage. It will join consecutive bases with the same coverage, and can be used to only print a BED file with the regions having a specific coverage range. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | The software has been downloaded 1000 times from BioConda |
| URL | https://bioconda.github.io/recipes/covtobed/README.html |
| Description | Bioinformatics workshop at the Evergreen Phage Meeting |
| 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 | 30 postgraduate students and early career researchers attended a workshop on the use of command-line tools in the analysis of virome data, as part of the Evergreen International Phage Biology meeting in Olympia, WA, USA |
| Year(s) Of Engagement Activity | 2019 |
| Description | Coffee Break Science |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | About 100 QIB Employees attended the Coffee science meeting to hear a talk on in vitro models of human gut including hte latest developments on gut-on-chop technology. There was lots of interest by my colleagues to learn about it, they were asking about applications, training, feasibility, etc. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://web.microsoftstream.com/video/77f38d25-d223-4b59-8a61-73d85c6b77fe |
| Description | Emulate Visit |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | About 15 staff from QI have attended the Emulate visit which took place at QIB with the intention to develop further collaboration and implementation of gut-on-chip tehnology at our Institute on a larger scale. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://intranet.nbi.ac.uk/infoserv/cgi-bin/ResearchOutcomes/view.asp?ID=63775 |
| Description | Invited lecture 23rd Biennial Evergreen International Phage Biology Meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Invited lecture on phage taxonomy. The audience reported increased understanding of the importance of phage taxonomy in data analysis and changing behaviours. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Lotus tutorial |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | A hands-on session for 20 PhD students and Master Students on how to analyse metabarcoding experiments using Lotus. This allowed to showcase a tool currently developed at the Quadram Institute and to engage in discussions with future researchers interested in microbiome experiments. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://github.com/telatin/lotus-tutorial |
| Description | Postgraduate Student Knowledge Exchange Trip to University of Parma, Italy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The Knowledge Exchange Trip is a yearly exchange visit with a University or institute in Europe which has a similar research focus to Quadram Institute Bioscience (QIB). The purpose of the trip, is for students to present their PhD research projects to a group of students and group leaders from the host institute and then the host institutes students also present their research to the QIB students. The students also receive a tour of the facilities at the host institute. 11 students attended the trip and gained experience presenting their research to an audience that does not necessarily specialise in the same area of research as them. Students gained knowledge of other research areas and also learnt about new techniques that could benefit their own research. It was also an opportunity to promote QIB and the excellent research that goes on within the institute, which may lead to future collaborations between QIB and the University of Parma. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Video for BioRepository |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Study participants or study members |
| Results and Impact | I took part in making a video for the BioRepository webpage to explain the importance of research and how collaboration with the biorepository improves the research we can deliver on the park to benefit the wider community. The use of state of the art in vitro gut models (including gut on chip) was metnioned. The videos were recorded back in November and are currently in the process of editing. Once they go live, the activity will reach a lot more people than listed above for this point in time. |
| Year(s) Of Engagement Activity | 2020 |