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

NameExpertiseCommunication channels
In order of preference
Martin Larralde
Updated
Using specialised research software, Programming languages, Cluster computing, Command-line computing, Cloud computing, Data management and curation, Software project management, Text mining, Benchmarking bioinformatics tools, Web technologies, Metagenomics and other meta-omics-
Georg Zeller
Updated
Using specialised research software, Exploratory data analysis and visualisation, Programming languages, Statistics and machine learning, Computational workflow management, Data management and curation, Software project management, Benchmarking bioinformatics tools, Transcriptomics, Genomics and comparative genomics, Metagenomics and other meta-omics

metagenomics, exploratory data analysis, applied statistics and machine learning
E-mail, Video Call – Monday 14:00 – 16:00
Mattia Forneris
Updated
Using specialised research software, Exploratory data analysis and visualisation, Programming languages, Statistics and machine learning, Command-line computing, Computational workflow management, Biological networks analysis, Transcriptomics, Genomics and comparative genomics, Cancer genomics and personalised medicine

Python, bash, snakemake, basic stats, RNA-Seq, variant discovery
Video Call, e-mail, EMBL Chat
Matthias Monfort
Updated
Programming languages, Cluster computing, Computational workflow management, Software project management, Web technologies, System administration

Nextflow & Galaxy (for NGS Workflow management), Javascript (front-end development e.g. eith Vue), Apache (web server setup), R/Rstudio setup, Unix)
Nicolas Descostes
Updated
Using specialised research software, Exploratory data analysis and visualisation, Programming languages, Cluster computing, Command-line computing, Computational workflow management, Software project management, Transcriptomics

NGS Analysis, R, Galaxy
E-mail, Video Call on request
Jure Pečar
Updated
Cluster computing, Command-line computing, Cloud computing, GPU computing, Benchmarking bioinformatics tools, System administration

HPC computing, software compilation
IT Ticket, EMBL Chat
Renato Alves
Updated
Using specialised research software, Exploratory data analysis and visualisation, Programming languages, Statistics and machine learning, Cluster computing, Command-line computing, Computational workflow management, Cloud computing, Data management and curation, Software project management, Biological networks analysis, Benchmarking bioinformatics tools, Web technologies, System administration, Transcriptomics, Genomics and comparative genomics, Proteomics and protein analysis, Metagenomics and other meta-omics, Structural biology

Python, metagenomics, NGS, NGLess, jug, git, Linux
Bio-IT drop-in sessions: Tuesdays 10:00-12:00, EMBL Chat
Jelle Scholtalbers
Updated
Using specialised research software, Programming languages, Cluster computing, Command-line computing, Computational workflow management, Cloud computing, Data management and curation, Software project management, Web technologies, System administration

Galaxy, Python, Git/Gitlab/GitlabCI/etc, (bio)conda, data management, bash, cluster
EMBL Chat, Video Call on request
Jean-Karim Heriche
Updated
Exploratory data analysis and visualisation, Programming languages, Statistics and machine learning, Image analysis, Cluster computing, Command-line computing, Computational workflow management, Cloud computing, Data management and curation, Software project management, Biological networks analysis, Web technologies, System administration, Genomics and comparative genomics, Proteomics and protein analysis, Bioimaging, Structural biology

Data analysis & integration, statistics, machine learning, R, perl, web development, databases
E-mail, EMBL Chat, Video Call on request
Eva Geissen
Updated
Using specialised research software, Programming languages, Biological modelling

mathematical modeling of biological systems, MatLab
Video Call – contact by e-mail to schedule
Lisanna Paladin
Updated
Using specialised research software, Programming languages, Cluster computing, Command-line computing, Cloud computing, Data management and curation, Software project management, Biological networks analysis, Biological modelling, Web technologies, Proteomics and protein analysis, Structural biology-
Christian Tischer
Updated
Using specialised research software, Exploratory data analysis and visualisation, Programming languages, Image analysis, Cluster computing, Command-line computing, Software project management, Bioimaging

Bioimage analysis, ImageJ, CellProfiler, Java
Video Call – contact by e-mail to schedule
Anthony Fullam
Updated
Exploratory data analysis and visualisation, Programming languages, Cluster computing, Command-line computing, Computational workflow management, Cloud computing, Data management and curation, Software project management, Benchmarking bioinformatics tools, Web technologies, System administration, Genomics and comparative genomics, Cancer genomics and personalised medicine, Metagenomics and other meta-omics-
Charles Girardot
Updated
Using specialised research software, Exploratory data analysis and visualisation, Programming languages, Statistics and machine learning, Cluster computing, Command-line computing, Computational workflow management, Data management and curation, Software project management, Web technologies, System administration, Transcriptomics, Genomics and comparative genomics

NGS Analysis, R, Java, Galaxy, bash, data management
E-mail, EMBL Chat
Wasiu AkanniPython, Phylogenetics, Bash, Conda, Perl, Mysql, HPC
Toby HodgesPython, Git/GitLab/GitHub/GitLab/Hub Pages, BashBio-IT drop-in sessions: Tuesdays 10:00-12:00
Mike SmithR, Bioconductor, HPC
Thomas SchwarzlR, Snakemake
Thea Van RossumR, microbiome data analysis, data wrangling, data visualization, basic statsVideo Call – contact by e-mail to schedule
Valentyna ZinchenkoPython, Bash, Deep learning, Image analysis, Image classificationE-mail
Nicolai Karchermetagenomics, microbiome data analysis, R, python, bash, data wrangling, data visualization, basic statsEMBL Chat or e-mail, Video Call on request
Nicola De MaioPhylogenetics, population genetics, statistical genetics, molecular evolution, molecular epidemiology, mathematical modelling
Aleix Lafita-Masip
No longer at EMBL
Sequence 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
Matt Rogon
No longer at EMBL
Network 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
Mathias Saver
No longer at EMBL
R, RNA-seq, ChIP-seq, ATAC-seq , Transposable element expression analyses
Anthony FullamPython, Nextflow, Bash, Conda, NGS, Cancer Genomics, HPCEMBL Chat or e-mail, Video Call on request
José Guilherme de AlmeidaPython (machine-learning, deep-learning, computer vision), R (machine-learning, data manipulation/wrangling, data-viz, basic stats)
Josep Manel Andrés MoscardóKubernetes, CloudIT Ticket, EMBL Chat
Jonas Hartmann
No longer at EMBL
Python, data science, image analysis, machine learning, data visualization, developmental biologyVideo Call, EMBL Chat, e-mail
Harald VohringerPython (tensorflow, pytorch, numpy, pandas)
Florian Huber
No longer at EMBL
R, 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
Dominik Kutrailastik, Python, Python image analysis, conda
Constantin PapeDeep learning, (large-scale) image analysis, Python, C++
Christian ArnoldR, RNA-seq, ChIP-seq, ATAC-seq analyses
Lena Čalyševa
No longer at EMBL
python, protein sequence and structure analysisE-mail, Video Call on request