ELIXIR UK - Industry Engagement sector Gabriella Rustici School of Biological Sciences

Activities so far 1.Appointed an Industry Engagement advisory committee 2.Circulated two surveys to: help us to understand the bioinformatics-related training needs of industry and consequently ensure that suitable training activities are developed and honed to target such needs. One survey targeted bioinformaticians, the other wet-lab scientists

Industry Engagement Advisory Committee Confirmed: Claus Bendtsen, AstraZeneca Mark Forster, Syngenta Samiul Hasan, GSK Wendy Filsell, Uniliver William Spooner, Eagle Genomics To be confirmed: Audrey Kauffmann, Novartis Justin Powell, Takeda Anthony Rowe, Janssen (declined)

Bioinformaticians survey results (62 responses) Q4. What is the size of the company you work for? Large company 71% SME 29% Q6. What is your discipline of interest? Bioinformatics48.4% Genomics12.9% Biomedical Sciences11.3% Toxicology6.5% Molecular Biology4.8% Computer Science1.6%

Bioinformaticians survey results Public repositories Software tools Programing languages

Bioinformaticians survey results Q8. Which competencies do you consider to be most crucial for your work? Data mining of large biological data-sets79.5% Ability to use statistical analysis software packages71.8% Use of scripting languages64.1% Integrating public and private data-sets61.5% Programming53.8% Modeling and warehousing of biological data48.7% Retrieving and manipulating data from public repositories46.2% Working with high-performance computing or cloud based solutions46.2% Version control tools33.3% Using and applying standards25.6% Using and building ontologies15.4% Other (please specify)5.1%

Bioinformaticians survey results Q9. Which bioinformatics training would you most value in relation to your work? Q. 11 How would you prefer training to be delivered to you? Data analysis skills76.9% Statistical methodologies69.2% Use of data standards in curation and/or data integration practices33.3% Programming skills28.2% Basic computing skills17.9% Other (please specify)12.8% Face-to-face training courses on site53.8% Face-to-face combined with online53.8% Online/eLearning48.7% Face-to-face training courses off site41.0%

Bioinformaticians survey results Q10. What topics would you like to see covered in future training activities?

Wet-lab scientists survey results (63 responses) Q4. What is the size of the company you work for? Large company: 98% SME: 2% Q6. What is your discipline of interest? Biomedical Sciences43.5% Molecular Biology38.7% Bioinformatics32.3% Genomics30.6% Biochemistry/Biophysics25.8% Medicine12.9% Computer Science12.9% Microbiology9.7% Toxicology8.1% Plant Sciences1.6%

Wet-lab scientists survey results Q8. Do you use software to analyze your data? Q9. Do you have any experience with writing programs to analyze your data? Yes 31%No 69% Microsoft software (e.g. Excel)84.3% Sequence alignment, similarity & homology tools (e.g. Blast, Clustal,...)45.1% Data analysis environments (e.g. R/Bioconductor, Matlab,....)27.5% Pathway & network analysis tools (e.g. Cytoscape, Biocarta, Ingenuity,...)19.6% Next generation sequencing read alignment and assembly programs (e.g. BWA, Bowtie,...)11.8% Gene set enrichment testing tools (e.g. DAVID)9.8% No, I do not use any software7.8% Workflow tools (e.g. Galaxy)5.9%

Q10. Do you collaborate with a bioinformatician/statistician on the analysis of your data? Q11. How confortable are you with statistics? Yes, I have a bioinformatician in the group that helps me to design experiments and also provides support for the data analysis39.2% Yes, occasionally I interact with a bioinformatician/statistician at my Institute, particularly when I get stuck and I don’t know how to proceed.31.4% No, I do not have any support. I am responsible for analyzing the data that I generate.27.5% No, the data analysis is carried out by someone else. I just receive a file with the results.2.0% Not so confident62.7% Confident25.5% Very confident7.8% I am not even sure of what statistics I need to know3.9% Wet-lab scientists survey results

Q12. Do you use scientific databases? Literature services (e.g. Pubmed,...)84.3% Protein databases (e.g. Uniprot, Pfam, Intact,...)45.1% DNA & RNA databases (e.g. Ensembl, 1000 genomes, UCSC,....)37.3% Ontology resources (e.g. Gene Ontology,..)27.5% Gene expression databases (e.g. ArrayExpress, Gene Expression Omnibus,...)25.5% Structures databases (e.g. PDBe)25.5% Systems databases (e.g. BioModels, Reactome, KEGG,...)13.7% Chemical biology databases (e.g. ChEMBL,..)7.8% Other databases, please specify7.8% No, I do not use databases2.0% Wet-lab scientists survey results

Q13. What expertise would you like to acquire to be able to better handle the data that you generate? Q14. How would you prefer training to be delivered to you? Face-to-face training courses on site64.7% Face-to-face combined with online43.1% Online/eLearning39.2% Face-to-face training courses off site21.6% Statistical knowledge (e.g. what statistics do I need to know to be able to analyze my data?)66.7% Data visualization skills (e.g. how does my data look like? How do I interpret and present my data?)66.7% Data manipulation skills (e.g. what software is more appropriate to analyze my data? How does a specific software work?)58.8% Scientific knowledge (e.g. how should I design my experiment to obtain meaningful results?)51.0% Data publishing skills (e.g. how do I publish my results?)33.3% Wet-lab scientists survey results

Training activities/initiatives with an Industry focus To name a few categories: Face-to-face workshops: e.g. EBI industry program, TGAC Grants for developing training solutions with an industry focus/support students training in Industry: e.g. BBSRC Modular Training Partnerships, MRC Industrial CASE studentships, BBSRC Industrial CASE, Industrial CASE Partnership Awards Stakeholder groups: e.g. Pistoia alliance, MRC training & careers groups Training activities within Industry: e.g. Life technologies

Various considerations Hold the first Advisory committee meeting within the next six months Collate all Industry use cases already available to define key competencies in Industry and disseminate these to all other sectors Utilize this information to prioritize key training areas Collaborations with other Elixir nodes: ELIXIR-NL will use the same surveys to assess the training needs of industry; share the results and collate more information – perhaps this should be done with all Elixir nodes? Engage Industries beyond pharma?