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.

Publications

10 25 50
publication icon
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 03/2018 
End 03/2021
 
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.