Grassroots consulting

In order to support computational work during COVID-19 times, members of EMBL's bio-computational community have come together and volunteered to provide assistance on a wide range of topics.

If you need help with any of the listed topics, reach out to our team of supporters on their preferred communication channel (e-mail if not specified).
Check also the online events calendar for drop-in times (currently 1-2 hours a week) and connection details.

If you want to join the team of helpers, contact Renato Alves and Lisanna Paladin via email and mention the topics you'd like to provide help on .
You will also find some of us on the EMBL chat and EMBL GitLab decorated with 🌱 to indicate the grassroot consultant status.

Our team of supporters

Name & contact infoTopicsPreferred communication channel
(by order of preference)
Aleix Lafita-MasipSequence homology search (HMMs, Pfam, MSAs), protein structure (Pymol, GROMACS, modelling), R data analysis (ggplot, igraph, statsE-mail, Video Call – contact by e-mail to schedule
Anthony FullamPython, Nextflow, Bash, Conda, NGS, Cancer Genomics, HPCEMBL Chat or e-mail, Video Call on request
Charles GirardotNGS Analysis, R, Java, Galaxy, bash, data managementE-mail, EMBL Chat
Christian ArnoldR, RNA-seq, ChIP-seq, ATAC-seq analyses
Christian TischerBioimage analysis, ImageJ, CellProfiler, JavaVideo Call – contact by e-mail to schedule
Constantin PapeDeep learning, (large-scale) image analysis, Python, C++
Dominik Kutrailastik, Python, Python image analysis, conda
Eva Geissenmathematical modeling of biological systems, MatLabVideo Call – contact by e-mail to schedule
Florian HuberR, basic stats, ML, data visualisation, data wrangling in all forms, data integration, databases, bash, Python/ImageJ for image segmentation/quantificationE-mail, Video Call – on request, EMBL Chat
Georg Zellermetagenomics, exploratory data analysis, applied statistics and machine learningE-mail, Video Call – Monday 14:00 – 16:00
Harald VohringerPython (tensorflow, pytorch, numpy, pandas)
Jean-Karim HericheData analysis & integration, statistics, machine learning, R, perl, web development, databasesE-mail, EMBL Chat, Video Call on request
Jelle ScholtalbersGalaxy, Python, Git/Gitlab/GitlabCI/etc, (bio)conda, data management, bash, clusterEMBL Chat, Video Call on request
Jonas HartmannPython, data science, image analysis, machine learning, data visualization, developmental biologyVideo Call, EMBL Chat, e-mail
Josep Manel Andrés MoscardóKubernetes, CloudIT Ticket, EMBL Chat
José Guilherme de AlmeidaPython (machine-learning, deep-learning, computer vision), R (machine-learning, data manipulation/wrangling, data-viz, basic stats)
Jure PečarHPC computing, software compilationIT Ticket, EMBL Chat
Lena Čalyševapython, protein sequence and structure analysisE-mail, Video Call on request
Mathias SaverR, RNA-seq, ChIP-seq, ATAC-seq , Transposable element expression analyses
Matthias MonfortNextflow & Galaxy (for NGS Workflow management), Javascript (front-end development e.g. eith Vue), Apache (web server setup), R/Rstudio setup, Unix)
Mattia FornerisPython, bash, snakemake, basic stats, RNA-Seq, variant discoveryVideo Call, e-mail, EMBL Chat
Matt RogonNetwork analysis, database mining, multi-omic data integration, visualisation, enrichment analysis (ontologies – drug, disease, GO etc., pathways, R, Cytoscape, GephiVideo Call – contact by e-mail to schedule, EMBL Chat
Mike SmithR, Bioconductor, HPC
Nicola De MaioPhylogenetics, population genetics, statistical genetics, molecular evolution, molecular epidemiology, mathematical modelling
Nicolai Karchermetagenomics, microbiome data analysis, R, python, bash, data wrangling, data visualization, basic statsEMBL Chat or e-mail, Video Call on request
Nicolas DescostesNGS Analysis, R, GalaxyE-mail, Video Call on request
Renato AlvesPython, metagenomics, NGS, NGLess, jug, git, LinuxBio-IT drop-in sessions: Tuesdays 10:00-12:00, EMBL Chat
Thea Van RossumR, microbiome data analysis, data wrangling, data visualization, basic statsVideo Call – contact by e-mail to schedule
Thomas SchwarzlR, Snakemake
Toby HodgesPython, Git/GitLab/GitHub/GitLab/Hub Pages, BashBio-IT drop-in sessions: Tuesdays 10:00-12:00
Wasiu AkanniPython, Phylogenetics, Bash, Conda, Perl, Mysql, HPC
Valentyna ZinchenkoPython, Bash, Deep learning, Image analysis, Image classificationE-mail