GSK Bio-Manufacturing Omics Data Challenge

GSK has a dataset of metabolomic, proteomic, transcriptomic analyses of fed-batch cultures of E. coli, producing two different fusion proteins under multiple bio-reactor conditions.

In the spirit of open-source science and our commitment to helping people Do More, Feel Better, and Live Longer, we are making this data set available to external parties for research. A research proposal is the key to unlock access.

We invite participants to submit proposals for innovative ways to analyse large datasets from fermentation batch experiments. Successful proposals will offer approaches likely to give useful insights from the data set and/or give insights to help solve important problems in bio-manufacturing.

Webinar with GSK

If you would like to hear GSK Vaccines talking about the Challenge, the data set and what to include in a proposal listen to Rui Portela, Senior Data Scientist, and Julia Pence Digital Transformation Portfolio Manager, in the recording of the webinar.

Three (3) proposals will be awarded 7000 Euro each and the winners will present their analysis and discuss its applications in pharmaceutical biomanufacturing with the GSK Vaccines Technical Development and Global Data Analytics departments. In addition, GSK may make funding available for possible joint collaboration projects with the Award winners if the initial analysis shows promising applications for GSK biomanufacturing or research.

Additionally, reasonable proposals from reputable submitters (who are not selected as winners) will also be given access to the data and be allowed to conduct their own independent research on the data.

Entries from academic researchers, companies, research institutes, start-ups and individuals are welcome.

Anti-bribery and corruption laws mean that any potential conflict of interest needs to be avoided, as such we cannot accept proposals from:

• Government officials holding a legislative, administrative or judicial position (see full definition in the challenge Terms and Conditions)
• Healthcare providers who prescribe or recommend GSK products
• External Experts that have the actual or perceived capacity, to influence or take official decisions affecting GSK business.

GSK are interested in novel approaches that integrate data across layers to give new insights: This might include, but is not limited to, models that allow:

• Integrated modelling of the cell metabolism based on multiple layers of data (for example, metabolite concentration to gene expression)
• Systematic identification of the interaction between variables at the different layers
• Prediction of the phenotype based on the genotype
• Modelling of cell metabolism and protein expression
• Understanding of the links between bioreactor conditions, gene and resulting protein expression
• Identification of variables that favor protein truncation, aggregation, frameshift…
• Increase ability to reduce frameshift, truncation, aggregation
• Use the dataset to validate fermentation models
• Other approaches not mentioned above

The following approaches are not of interest. They will not be selected for the GSK award. However, access to the data may be possible if the submitter can explain the reasons for access, e.g. for education/training of PhD students.

• Design of experiments to improve process
• Standard regression and statistical correlation assessment between the given variables
• Reduced process level modelling that for example only leverage the link between glucose substrate feeding and cellular growth

A panel of GSK subject matter experts will review the proposals and select the winners based on:

• Unique approach to combining data sets to generate new insights
• Applicability of approach to problems commercially relevant to GSK
• Ability of proposal team to execute proposed approach

You must complete and submit the online response form by October 14, 2021 by 5:00 PM EST. You will be able to upload additional documents with your response. In your concise, non-confidential response you should include:

• Overview of the proposed study, including: aims, approach, what is unique about the approach, how the approach uses different data types to create integrated models
• Explain how the GSK data will enable the proposed study to accomplish the goals
• Past achievements and list of references that support your proposed study (optional)
• Brief description of the team behind the proposal
  • CV of lead researcher

By submitting a proposal, respondents agree to the Challenge Terms and Conditions and to the submission requirements, including confidentiality, selection, and review process.

Data Access

Selected applicants (both challenge winners and data users) can use the data under the Challenge Terms and Conditions. After the Terms and Conditions are agreed selected applicants will get access to the data via secure servers.

GSK will not claim IP on the analyses or algorithms developed by use of the data, however winners will explain to GSK how the analyses was performed such that GSK may use, repeat, or modify the analyses with this or other data.

Results obtained by use of the data may be published with acknowledgement of GSK being the source of the data.