India-United Kingdom Bioinformatics Network
Lead Research Organisation:
The Pirbright Institute
Department Name: Pirbright Laboratory
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 |
| Jan Kim (Principal Investigator) | |
| Venugopal Nair (Co-Investigator) |
Publications
Ramakrishnan E
(2021)
GAMUT: A genomics big data management tool
in Journal of Biosciences
| Description | Partners in Pune and at the Pirbright Institute have collaborated to identify single nucleotide polymorphisms (SNPs) in 8 experimental chicken lines from next generation sequencing (NGS) data, and we have developed a database of these SNPs. Such polymorphisms (genetic differences) can be correlated or causal to a bird's resistance to viral diseases (e.g. influenza, Marek's disease). At this stage we work to exploit the database for finding such SNPs related to various features relevant to disease resistance. |
| Exploitation Route | The SNP database can be mined for numerous further genetic determinants of phenotypic traits in general, i.e. it is not restricted to resistance to viral diseases. Additionally, the software is designed to be capable of adding SNPs from further chicken lines. |
| Sectors | Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology |
| URL | https://github.com/bio-cdac/SNPdb_MongoDB |
| Description | Re-sequencing data of experimental chicken lines maintained at The Pirbright Institute have been processed in collaboration with Indian partners in Pune. Since Oct 2014 these are available to researchers at the Institute internally. Additional tools (SNP database) are currently being added to the resource already provided, following a recent collaborative visit in Jan 2016. The work has continued throughout 2016, and in Jan 2017 a workshop on NGS data analysis has been held as a satellite event to the Accelerating Biology 2017 conference in Pune. |
| First Year Of Impact | 2016 |
| Sector | Pharmaceuticals and Medical Biotechnology |
| Description | Dissecting the molecular pathways of MDV oncoprotein Meq for understanding pathogenesis and aid vaccine development |
| Amount | £440,000 (GBP) |
| Funding ID | BB/R007896/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2018 |
| End | 03/2021 |
| Description | India-United Kingdom Bioinformatics Network |
| Amount | £25,000 (GBP) |
| Funding ID | BB/K021362/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2013 |
| End | 02/2018 |
| Description | Innovations in control of avian infectious diseases for sustainable growth and food security in low and middle income countries |
| Amount | £355,000 (GBP) |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 12/2016 |
| End | 11/2021 |
| Title | chicksnp |
| Description | A database of SNPs identified on the basis of Next Generation Sequencing data from 8 experimental chicken lines |
| Type Of Material | Database/Collection of data |
| Provided To Others? | No |
| Impact | SNP data is currently used in internal collaborations with The Pirbright Institute |
| URL | https://github.com/jttkim/chicksnp |
| Description | Global Alliance for Research on Avian Diseases |
| Organisation | Global Alliance for Research on Avian Diseases |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | This alliance led by Pirbright has participation from over 40 countries and comprises of academics and industry professionals. This forum helps in working together, identifies the challenges and opportunities for improved control of avian diseases |
| Collaborator Contribution | Two successful international meetings were organised as part of this alliance, one in London in 2015 and most recent one in Hanoi, Vietnam in January 2018 |
| Impact | Organisation of two successful international meetings and development of significant collaborations |
| Start Year | 2015 |
| Title | SNPdb_MongoDB |
| Description | Single Nucleotide Polymorphism (SNP) database for chicken lines, based on MongoDB |
| Type Of Technology | Software |
| Year Produced | 2016 |
| Open Source License? | Yes |
| Impact | This system is available in the Pirbright Institute internally, where it represents progress over legacy systems. Opportunities of adding SNPs further chicken lines and to develop SNPdb_MongoDB into a general purpose system are being explored. |
| URL | https://github.com/bio-cdac/SNPdb_MongoDB |
| Description | Collaborative Visit to C-DAC |
| 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 | Visit to partners in India to plan software development for the year 2016 ahead. |
| Year(s) Of Engagement Activity | 2016 |
| Description | India-UK Bioinformatics Workshop 2018 |
| 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 | Bioinformatics scientists, practitioners and users of bioinformatics applications from India and the UK came together for a one day workshop. Common interests in areas including food security, big data analytics and drug development were identified and discussed. Training in bioinformatics was highlighted as a key requirement, and suggestions to meet these by mutual visits and exchange programmes were developed. A report summarising these discussions is being prepared and will be made available to India's DBT and the UK's BBSRC. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Invitation to give keynote talk on 'Control of avian diseases: Challenges and opportunities' |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave the Keynote talk on 'Control of avian diseases: Challenges and opportunities' at this International Symposium organized with an aim to gather international virology experts from both human and veterinary fields to share research experience, update findings and contribute their expertise through presentation and interactive discussion. The topics will cover a wide range of virology research common in both human and animal aspects. In addition, technological platforms such as vaccine development, and novel assays will be emphasized and addressed. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.biotec.or.th/virus-symposium2018/index.php |
| Description | Invitation to talk at the Vaccine Symposium "Vaccines at different levels of complexity from subunit to whole cell formulations" jointly organised by the Centre of Genomic Regulation (CRG), Radboud UMC and MSD Animal Health, with the support from the MycoSynVac project |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave a talk and participated in the discussion on the challenges and research opportunities for innovation in poultry disease control |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.crg.eu/ |
| Description | Invited Talk at Accelerating Biology 2016 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation on some work with Indian partners, with a focus on reproducible scientific computing. Presentation was received with interest and resulted in an invitation to give similar presentation in Delhi. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Invited Talk at Accelerating Biology 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of work carried out at The Pirbright Institute and in collaboration with C-DAC |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://cdac.in/index.aspx?id=ev_symposium_2017 |
| Description | Invited to talk at the International Conference on Building Human and Animal Health Capacities organised by the Jordan University of Science and Technology |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Participated in the discussion and talked on 'The recent advances in vaccination-based control of poultry diseases'. The need for increased awareness of the pathogen diversity in the design of vaccines and the opportunities from advances in vaccine technologies were discussed |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.just.edu.jo/conferences/bhahc/Pages/default.aspx |
| Description | NGS Workshop at Accelerating Biology 2017 |
| 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 one-day workshop combining short introductory lectures of key computational approaches for NGS data analysis with practical demonstrations and exercises. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://cdac.in/index.aspx?id=ev_symposium_2017 |
| Description | Organisation of UK-India Bioinformatics Workshop |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The meeting discussed the challenges and opportunities and have decided to come up with a strategy document on working together between UK and India on data-driven biology |
| Year(s) Of Engagement Activity | 2018 |
| Description | Organised the 3rd UK-China CERAD meeting in Guildford, UK in July 2017 |
| 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 | The 3rd UK-China CERAD meeting helped to bring together professional from both countries to identify challenges and exploit the opportunities for improved control of poultry diseases and increasing food security. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.uk-china-cerad.org/ |
| Description | Organising and giving Keynote talk at the GARAD meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Global Alliance of Poultry industry professional and academia to discuss about the advances in control strategies of diseases |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://Garad.org |
| Description | Poultry Health course |
| 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 | Poultry Health Course is run as a residential and online course to transfer recent advances in avian disease research from the laboratory to the field. |
| Year(s) Of Engagement Activity | Pre-2006 |
| URL | http://www.poultryhealthcourse.com/ |
| Description | V Nair was invited to talk a the Poultry Health Workshop and Conference on 19th-20th Nov, 2018 in Kathmandu, Nepal |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | more than 100 stakeholders from different sectors of the Poultry industry and academia attended the meeting. There was engagement from the different sectors for initiating a combined approach for finding solutions |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.cmdn.org. |