CRG Bioinformatics Core:Jan - June 2015

• Consulting researchers on bioinformatics tools, data analysis, data management, and interpretation of experimental data.

• Analyzing of high-throughput sequencing data and conducting transcriptomics and downstream analysis.

• Developing ad hoc databases and web interfaces.

• Providing bioinformatics training and cataloguing “know-how” expertise.

• Implementing and developing new bioinformatics technologies.

• Collaborating with research groups.

Bioinformatics Core’s Mission – To contribute to the CRG’s research

excellence by:

Personnel capacity (80% of full time)

• Jan - March: 893 hrs– Luca Cozzuto: 189 hrs (50% as an acting head)– Sarah Bonnin: 384 hrs– Toni Hermoso: 320 hrs

• April - June: 1331 hrs– Luca Cozzuto: 365 hrs– Sarah Bonnin: 358 hrs– Toni Hermoso: 358 hrs– Carlos Company: 250 hrs (starting May 1)

Counting hours (Jan - June 2015)

Hours

% capacity (2224 hrs)

Closed requests (customers already paid)

700 32%

Open requests (customers & internal development)

568 25%

Saca La Lengua project 606 27%

¢1-tasks (seminars, training, reading, discussions, etc.)

350 16%

Closed requests (% hours) by type of analysis

RNA-seq32%

genome assembly

23%

ChIP-seq20%

database19%

microarray2%

HTqPCR2%

PI Amount Institution Customer Type manual hours Type analysisBill Keyes 70.2 CRG PRBB 5 microarrayBill Keyes 216.28 CRG PRBB 9 RNA-seqBill Keyes 171.29 CRG PRBB 12 downstream analysisEduard Sabido 154.44 CRG PRBB 11 databaseFernando Giraldez 180.1 UPF PRBB 9 ChIP-seqFyodor Kondrashov 966.08 CRG PRBB 56 genome assemblyGloria Sans Fons 328.28 UB external 53 ChIP-seqJames Sharpe 1384.8 CRG PRBB 53 RNA-seqJose Ayte 577.77 UPF PRBB 21 RNA-seqJosep Comin 271.81 IMIM PRBB 16 HTqPCRLuis Serrano 292.05 CRG PRBB 19 downstream analysisLuis Serrano 586.91 CRG PRBB 38 genome assemblyLuis Serrano 1415.02 CRG PRBB 95 databaseManuel Ernesto Mendoza 758.26 CRG PRBB 44 ChIP-seqManuel Esteller 408.11 IDIBELL external 8 RNA-seqMaria Pia Cosma 467.5 CRG PRBB 34 RNA-seqMilana Morgenstern 4478.07 CNIO external 42 RNA-seqMònica Morales 140.4 CRG PRBB 11 databaseMontserrat Sanchez Cespedes 306.08 IDIBELL external 6 microarrayPedro Carvalho 441 CRG PRBB 17 RNA-seqSandra Peiro 462.12 IMIM PRBB 24 ChIP-seqSusana De la Luna 84.24 CRG PRBB 6 microarrayVivek Malhotra 455 CRG PRBB 22 RNA-seqXavier Estivill 1033.88 CRG PRBB 20 RNA-seqYogi Jäger 1620.68 CRG PRBB 69 genome assembly

17270.37 700

In 2015, 15 of CRG PIs have requested/received services

• Microbiome analysis (Saca La Lengua, lung microbiome) – set up three pipelines (CHIIME, mothur, Ribopicker), will be benhcmarked when the MOCK community is sequenced; set up metagenomics.biocore. crg.eu (resourcs, papers, protocols, software).

• RNA-seq analysis – setting up STAR-RSEM (Encode-3 official pipeline), kallisto (very fast mapper and quantifier), eXpress (efficient de novo transcript quantification).

• iCLIP data analysis (so far 3 PIs at CRG).

• OpenArray data analysis (miRNA profiling) (IMIM).

• Whole genome assembly & analysis (Opitz syndrome).

• Infrastructure for internal data integration, analysis, and management (Mycoplasma Big project, Sep 2015) – a new bioinformatician will be hired in Oct, 2015 (expertise?).

• Infrastructure for external data integration and collaboration with hospitals (submitted H2020 proposal, April 2015, PI Josep Roca, Hospital Clinic).

• Suggestions? Anticipation?

Current & Future Technology Development

• Catalogue of in-house developed software -- PIs’ vision?

• Catalogue of “know-how” bioinformatics protocols -- PIs’ vision?

• Bioinformatics Technical Club (PRBB/CNAG).

• CRG educational wiki-resource (with Elias Bechara).

• Planned courses for Fall 2015: UCSG Genome Browser, Setting up wiki-resource for project/lab management. Suggestions?

• Hosting PhD students (planned for Oct-Dec, 2015, 2m visit of the PhD student from Argentina to work on P. aeruginosa genome assembly and comparative analysis).

• Offering internships in the unit.

• Other?

Training, teaching and knowledge dissemination

Questions to the committee

• How to encourage PIs to include bioinformaticians providing "service" to the papers’ co-authors?

• How to promote the unit to participate in the internally developed software beta-testing and benchmarking?

• We need dedicated compute nodes!

• The fate of Galaxy? Alternatives?

• PIs’ support with the Bioinformatics Club and working groups.

• Which services PIs would be interested to outsource (rather than software maintenance)?

• What new technologies and services are anticipated?