Welcome to the CRG Bioinformatics Core!
We provide researchers with services of analyses of high-throughput sequencing (NGS, Nanopore, droplet-based) and other biomedical data, software/pipelines and database development, and bioinformatics training. We focus on delivering reproducible results using the modern computational solutions (NextFlow, Cloud, Linux containers). Contact us.
Data are provided at http://covid.crg.eu
and are analyzed using the MasterOfPores pipeline
developed by us in collaboration with Eva Novoa's group. The resource is listed by TransBioNet covid-19 research efforts
We are starting again our Introduction to R
internal course: 21 hours split in 6 half days!
On 10-13 February, 2020, we organized and delivered the RNA-Seq data analysis course
as part of the PHINDaccess
project at the Institut Pasteur
Today we started our Bioinformatics for Biologists
internal CRG course: 1.5h course weekly for the next 8 weeks. On the program: DNA, gene, and protein sequences, sequence comparison, gene sequences, annotation, gene and protein function.... and more!
Last week we participated at the 4th TransBioNet meeting hosted at INCLIVA, Valencia, where we discussed the challenges in the Translational Bioinformatics field and what can be done to empower bioinformaticians in these environments.
Press release about the event: https://inb-elixir.es/index.php/news/la-red-de-bioinformatica-traslacional-transbionet-reune-en-incliva-un-destacado-grupo-de
Luca presented the "Master of pores" Nextflow
pipeline at the PRBB computational genomics seminar.
We attended the PHINDaccess
project annual meeting organized by the Institut Pasteur de Tunis
(IPT) in Monastir, Tunisia. The project is lead by the IPT in collaboration with the CRG, the Institut Pasteur
, the Robert Koch Institute
(RKI) and the Max-Planck-Institute for Molecular Genetics
Today we published in bioRxiv
the first Nextflow
pipeline about analysis of Nanopore sequencing datasets, in collaboration with the Novoa lab
We hosted this year's Core4Life
Bioinformatics & Scientific Computing Working Group at the CRG. Great brainstorming sessions and interactions with computational biologists from VIB, IMP, MBI-CBG, Institut Curie, FGCZ, EMBL Heidelberg, Institut Pasteur and BIH.
Today we welcome the Dr Sarah Mwangi from the University of Pretoria, in the Biocore. She will stay with us for the next 6 months to work on the avocado genome, thanks to the "Mujeres por Africa"
Toni attended the EuroSciPy 2019 conference
, the 12th European Conference on Python in Science.
Sarah attended the useR! 2019 conference
in Toulouse, France. useR! is the largest R statistical language conference organized world wide.
On June 13-14, 2019 we provided a third edition of a hands-on workshop on the Linux containers (Docker and Singularity). Participation was open to the BIST and PRBB institutions. The materials of the course are available in this GitHub repository
. This time Singularity introduction was provided by Carlos Eduardo Arango Gutierrez, software engineer at Sylabs, the company supporting Singularity (his contents here
We offered a new RNA-seq course to the PRBB community: 14 hours of theory/hands on and a 4-hour session to discuss a small RNA-seq project analyzed by the trainees. The material is available on our github
This week we gave a Linux course for biologists, focused on genomics data format and parsing (first edition!). The material is available here: https://biocorecrg.github.io/advanced_linux_2019/
We just finished providing a 28-hour course over 4 weeks to 19 trainees: check the material! https://biocorecrg.github.io/CRG_RIntroduction/
On January 28-29, 2019 we provided a second edition of a hands-on workshop on the Linux containers (Docker and Singularity). Participation was open to the BIST and PRBB institutions. The materials of the course are available in this GitHub repository
. This time Singularity introduction was provided by David Godlove, software engineer at Sylabs, the company supporting Singularity (his contents here
On December 11-12, 2018 we provided the first edition of a hands-on workshop on the Linux containers (Docker and Singularity). Participation was open to the BIST institutions
. The materials of the course are availble in this GitHub repository
The next edition of the course will take place on January 28-29, 2019.
From October 4th to October 5th 2018 we shared with the rest of participants of "Open Science: From values to practices
debate" our experience customizing and deploying different tools and frameworks for integrating Open Science
as part of our daily work.
We can now offer a new service at the bioinformatics unit: the ribosome profiling/Ribo-seq analysis: don't hesitate to contact us!
Sarah attended the 2018 edition of the "Networks & Pathways
" 4-day course at the EMBL-EBI
, Hinxton, UK.
Intense theoretical and hands on sessions on networks, pathways, graphs, provided by a great training team.
The BioCore, with the help and contribution of Rodny Hernández Coello, Luis Expósito Piñol, Emilio Palumbo, Paolo Di Tommaso, and Estefania Mancini, conducted today the first ever (it finally became actual!) CRG workshop on how to start a bioinformatics project, to handle files and directories, to use git, GitHub and containers, to pipeline, and where to find software and mirror databases on the cluster. The collected feedback will be used to plan more in-depth hands-on on these topics.
Toni and Luca pulled together a very well recieved hands-on workshop in Paris on April 6. More than 30 people from 6 bioinformatics facilities of the C4L alliance attended.
Code, instructions and slides are available at: https://github.com/biocorecrg/C4LWG-2018
As part of CRG outreach activities, with other researchers and center's communication and engangement team, we participated in a few hours debate about the scientific and ethical challenges of technologies such as CRISPR with a group of invited secondary school teachers.
As a part of the different activities on the International Day of Women and Girls in Science 2018 we supported a half-day Wikipedia editathon organised by the PRBB. More details
Toni Hermoso BioCore member guided a Wikipedia editathon on biosciences organised by the Catalan Society of Biology (SCB). Attending scientists learned how to start and edit Wikipedia articles and how to manage and provide relevant publication references. More information (in Catalan)
S-Biomedic NV, Belgium
, a startup that brings novel therapeutic and consumer solutions to the skin microbiome, became the user of our services.
As part of Open Access Week 2017 edition, Guillaume Filion (CRG PI) and Toni Hermoso (BioCore member) organised an introductory session about Open Science and Life Sciences
within the 2017 edition of OpenAire/Foster webinars. Slides
. More information at CRG website
This year Sarah won the CRG technician training award, which allowed her to attend the "Interactive Data Analysis and Visualization with R Shiny" organized in Hostalets de Pierola by Transmitting science
Great week of hands on (delivered by Ashton Drew from KDV decision analytics LLC
) that provides exciting new knowledge for the BioCore!
Julia gave a short 3-hr course on microbiome sequencing and analysis at the Bioinformatics Bootcamp for Engineers
organized by the Bioinformatics Barcelona Association (BIB)
The Vertebrate Alternative Splicing and Transcription Database (VastDB)
is the largest resource of genome-wide, quantitative profiles of AS events assembled to date. VastDB provides readily accessible quantitative information on the inclusion levels and functional associations of AS events detected in RNA-seq data from diverse vertebrate cell and tissue types, as well as developmental stages. Read the paper in Genome Research
This year retreat was organized by Julia, Romina Garrido, and Lucas Carey of UPF. It took place in Saint Feliu de Guixols of the Costa Brava in June 15-16, 2017. According to the survey of 79 participants, 87% found the retreat helpful for their studies/research, 75% enjoyed the grant proposal game that was the retreat's highlight, 91% liked the lightning talks sessions about the future and current research problems, and 90% agreed that the retreat program was balanced in terms of free/fun and scientific activities. And despite the problems with electricity going on and off during talks and a bad WiFi, everyone liked the venue. You can find the survey results here
We just finished the 3rd sequence of the CRG course Introduction to Biostatistics in R
ran in May-July 2017. More than 50 students attended 3 days of lectures and 31 hrs of hands-on practicums in R. The courses details can be found here
Julia and Sarah participated in the Core Facilities Management Workshop
, July 6-7, 2017, organized by and hold at CRG.
Dr. Elizabeth Balyejusa Kizito, Head of the Department of Agricultural Sciences, Uganda Christian University, is working together with the CRG Genomics and Bioinformatics units on the development of a robust set of genomic tools for more efficient breeding in Solanum aethiopicum
. The Women for Africa Foundation
is a Spanish private, non-profit entity created in February 2012 by María Teresa Fernández de la Vega, the former Vice President of the Government of Spain, with the aim of promoting African women’s leadership in scientific research and technology transfer. Read the El Periodico article here
Jason Limberis’ project concerned the in vivo transcriptional profiling of Mycobacterium tuberculosis from highly infectious TB patients. Melissa Nel, MD, has worked on WES and variant identification in treatment-resistant juvenile-onset ophthalmoplegic-complicated Myasthenia Gravis patients.
Toni talked about the browser-centered sequence analysis services.
Members of the CRG Core Facilities presented to the public the Saca La Lengua project
about the study of the mouth microbiome at the Barcelona Science Fair
The comprehensive resource of lncRNA localization in human cells, the LncATLAS database
, is based on RNA-sequencing data sets and contains 6768 GENCODE-annotated lncRNAs represented across various compartments of 15 cell lines. Read the paper published in RNA here
The title of the talk was Interactive Data Visualization: Visual and analytical insights into complex biological data.
The study, published in the journal Scientific Reports
, identifies the gene that causes Opitz C syndrome in the only patient diagnosed with this ultra-rare disorder in Catalonia, which affects only sixty people in the world. The identified mutation in the gene MAGEL2 coincides with the one seen in some patients with another minority disease, the Schaaf-Yang syndrome. Here is the link to the news on the CRG website
Luca presented the talk AnnoWiki: Genome annotation management system.