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 ID: 807014
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Slide1
CRG Bioinformatics Core:Jan - June 2015
Slide2Consulting 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:
Slide3Personnel capacity (80% of full time)Jan - March: 893
hrs
Luca Cozzuto: 189 hrs (50% as an acting head)Sarah Bonnin: 384 hrsToni 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)
Slide4Counting 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%
Slide5Closed requests (% hours) by type of analysis
Slide6PI
Amount
InstitutionCustomer Typemanual hoursType analysisBill Keyes
70.2
CRG
PRBB
5
microarray
Bill Keyes
216.28
CRG
PRBB9RNA-seqBill Keyes171.29CRGPRBB12downstream analysisEduard Sabido154.44CRGPRBB11databaseFernando Giraldez180.1UPFPRBB9ChIP-seqFyodor Kondrashov966.08CRGPRBB56genome assemblyGloria Sans Fons328.28UBexternal53ChIP-seqJames Sharpe1384.8CRGPRBB53RNA-seqJose Ayte577.77UPFPRBB21RNA-seqJosep Comin271.81IMIMPRBB16HTqPCRLuis Serrano292.05CRGPRBB19downstream analysisLuis Serrano586.91CRGPRBB38genome assemblyLuis Serrano1415.02CRGPRBB95databaseManuel Ernesto Mendoza758.26CRGPRBB44ChIP-seqManuel Esteller408.11IDIBELLexternal8RNA-seqMaria Pia Cosma467.5CRGPRBB34RNA-seqMilana Morgenstern4478.07CNIOexternal42RNA-seqMònica Morales140.4CRGPRBB11databaseMontserrat Sanchez Cespedes306.08IDIBELLexternal6microarrayPedro Carvalho441CRGPRBB17RNA-seqSandra Peiro462.12IMIMPRBB24ChIP-seqSusana De la Luna84.24CRGPRBB6microarrayVivek Malhotra455CRGPRBB22RNA-seqXavier Estivill1033.88CRGPRBB20RNA-seqYogi Jäger1620.68CRGPRBB69genome assembly17270.37700
In 2015, 15 of CRG PIs have requested/received services
Slide7Microbiome 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
Slide8Catalogue 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
B
echara
).
Planned courses for Fall 2015: UCSG Genome Browser, Setting up wiki-resource for project/lab management.
Suggestions?
Hosting PhD students (planned for Oct-
D
ec, 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
Slide9Questions 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?