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CRG Bioinformatics Core: Jan - June 2015. Consulting researchers on bioinformatics tools, data analysis, data management, and interpretation of experimental.

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Presentation on theme: "CRG Bioinformatics Core: Jan - June 2015. Consulting researchers on bioinformatics tools, data analysis, data management, and interpretation of experimental."— Presentation transcript:

1 CRG Bioinformatics Core: Jan - June 2015

2 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:

3 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)

4 Counting hours (Jan - June 2015) Hours% capacity (2224 hrs) Closed requests (customers already paid) 70032% Open requests (customers & internal development) 56825% Saca La Lengua project 60627% ¢1-tasks (seminars, training, reading, discussions, etc.) 35016%

5 Closed requests (% hours) by type of analysis

6 PIAmountInstitutionCustomer Typemanual hoursType analysis Bill Keyes70.2CRGPRBB5microarray Bill Keyes216.28CRGPRBB9RNA-seq Bill Keyes171.29CRGPRBB12downstream analysis Eduard Sabido154.44CRGPRBB11database Fernando Giraldez180.1UPFPRBB9ChIP-seq Fyodor Kondrashov966.08CRGPRBB56genome assembly Gloria Sans Fons328.28UBexternal53ChIP-seq James Sharpe1384.8CRGPRBB53RNA-seq Jose Ayte577.77UPFPRBB21RNA-seq Josep Comin271.81IMIMPRBB16HTqPCR Luis Serrano292.05CRGPRBB19downstream analysis Luis Serrano586.91CRGPRBB38genome assembly Luis Serrano1415.02CRGPRBB95database Manuel Ernesto Mendoza758.26CRGPRBB44ChIP-seq Manuel Esteller408.11IDIBELLexternal8RNA-seq Maria Pia Cosma467.5CRGPRBB34RNA-seq Milana Morgenstern4478.07CNIOexternal42RNA-seq Mònica Morales140.4CRGPRBB11database Montserrat Sanchez Cespedes306.08IDIBELLexternal6microarray Pedro Carvalho441CRGPRBB17RNA-seq Sandra Peiro462.12IMIMPRBB24ChIP-seq Susana De la Luna84.24CRGPRBB6microarray Vivek Malhotra455CRGPRBB22RNA-seq Xavier Estivill1033.88CRGPRBB20RNA-seq Yogi Jäger1620.68CRGPRBB69genome assembly 17270.37700 In 2015, 15 of CRG PIs have requested/received services

7 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

8 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

9 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?

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