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 | Expertise | Communication channelsIn order of preference |
|---|---|---|
| Martin LarraldeUpdated | 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 ZellerUpdated | 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-omicsmetagenomics, exploratory data analysis, applied statistics and machine learning | E-mail, Video Call – Monday 14:00 – 16:00 |
| Mattia FornerisUpdated | 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 medicinePython, bash, snakemake, basic stats, RNA-Seq, variant discovery | Video Call, e-mail, EMBL Chat |
| Matthias MonfortUpdated | Programming languages, Cluster computing, Computational workflow management, Software project management, Web technologies, System administrationNextflow & Galaxy (for NGS Workflow management), Javascript (front-end development e.g. eith Vue), Apache (web server setup), R/Rstudio setup, Unix) | – |
| Nicolas DescostesUpdated | Using specialised research software, Exploratory data analysis and visualisation, Programming languages, Cluster computing, Command-line computing, Computational workflow management, Software project management, TranscriptomicsNGS Analysis, R, Galaxy | E-mail, Video Call on request |
| Jure PečarUpdated | Cluster computing, Command-line computing, Cloud computing, GPU computing, Benchmarking bioinformatics tools, System administrationHPC computing, software compilation | IT Ticket, EMBL Chat |
| Renato AlvesUpdated | 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 biologyPython, metagenomics, NGS, NGLess, jug, git, Linux | Bio-IT drop-in sessions: Tuesdays 10:00-12:00, EMBL Chat |
| Jelle ScholtalbersUpdated | 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 administrationGalaxy, Python, Git/Gitlab/GitlabCI/etc, (bio)conda, data management, bash, cluster | EMBL Chat, Video Call on request |
| Jean-Karim HericheUpdated | 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 biologyData analysis & integration, statistics, machine learning, R, perl, web development, databases | E-mail, EMBL Chat, Video Call on request |
| Eva GeissenUpdated | Using specialised research software, Programming languages, Biological modellingmathematical modeling of biological systems, MatLab | Video Call – contact by e-mail to schedule |
| Lisanna PaladinUpdated | 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 TischerUpdated | Using specialised research software, Exploratory data analysis and visualisation, Programming languages, Image analysis, Cluster computing, Command-line computing, Software project management, BioimagingBioimage analysis, ImageJ, CellProfiler, Java | Video Call – contact by e-mail to schedule |
| Anthony FullamUpdated | 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 GirardotUpdated | 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 genomicsNGS Analysis, R, Java, Galaxy, bash, data management | E-mail, EMBL Chat |
| Mike Smith | R, Bioconductor, HPC | – |
| Thomas Schwarzl | R, Snakemake | – |
| Thea Van Rossum | R, microbiome data analysis, data wrangling, data visualization, basic stats | Video Call – contact by e-mail to schedule |
| Valentyna Zinchenko | Python, Bash, Deep learning, Image analysis, Image classification | |
| Nicolai Karcher | metagenomics, microbiome data analysis, R, python, bash, data wrangling, data visualization, basic stats | EMBL Chat or e-mail, Video Call on request |
| Nicola De Maio | Phylogenetics, population genetics, statistical genetics, molecular evolution, molecular epidemiology, mathematical modelling | – |
| Sequence homology search (HMMs, Pfam, MSAs), protein structure (Pymol, GROMACS, modelling), R data analysis (ggplot, igraph, stats | E-mail, Video Call – contact by e-mail to schedule | |
| Network analysis, database mining, multi-omic data integration, visualisation, enrichment analysis (ontologies – drug, disease, GO etc., pathways, R, Cytoscape, Gephi | Video Call – contact by e-mail to schedule, EMBL Chat | |
| R, RNA-seq, ChIP-seq, ATAC-seq , Transposable element expression analyses | – | |
| Anthony Fullam | Python, Nextflow, Bash, Conda, NGS, Cancer Genomics, HPC | EMBL Chat or e-mail, Video Call on request |
| José Guilherme de Almeida | Python (machine-learning, deep-learning, computer vision), R (machine-learning, data manipulation/wrangling, data-viz, basic stats) | – |
| Josep Manel Andrés Moscardó | Kubernetes, Cloud | IT Ticket, EMBL Chat |
| Python, data science, image analysis, machine learning, data visualization, developmental biology | Video Call, EMBL Chat, e-mail | |
| Harald Vohringer | Python (tensorflow, pytorch, numpy, pandas) | – |
| R, basic stats, ML, data visualisation, data wrangling in all forms, data integration, databases, bash, Python/ImageJ for image segmentation/quantification | E-mail, Video Call – on request, EMBL Chat | |
| Dominik Kutra | ilastik, Python, Python image analysis, conda | – |
| Constantin Pape | Deep learning, (large-scale) image analysis, Python, C++ | – |
| Christian Arnold | R, RNA-seq, ChIP-seq, ATAC-seq analyses | – |
| python, protein sequence and structure analysis | E-mail, Video Call on request | |