Our services
The Bioinformatics Core offers a wide range of services supporting research activities of the LCSB and international partners. We provide expertise and infrastructure supporting responsible and reproducible research, especially for computationally demanding and data-intensive activities.
Reproducible research
We offer support in setting up and conducting reproducible research by offering training, support, and tools for code and data of scientific projects. We also support the pre-publication check at LCSB, an initiative helping to deliver publications with reproducible results. Finally, we support LCSB with data stewardship services, helping to manage data produced during a scientific project, and their long-term storage and reuse.
| Service | Scope | Topic | Contact |
|---|---|---|---|
| Responsible and Reproducible Research (R3) | LCSB, University of Luxembourg | Training, tools Research support | Vilem Ded Miroslav Kratochvil |
| Pre-Publication check | LCSB | Publication quality check Research support | Vilem Ded Miroslav Kratochvil |
| Data stewardship | LCSB | Research data management | Vilem Ded |
| High-performance simulations of genome-scale metabolic models | LCSB, Worldwide | Personalised medicine Exascale computing | Sarah Peter Miroslav Kratochvil |
Training
We provide training for employees of the LCSB. Through the local ELIXIR node we provide training to the wider Luxembourgish research community. Topics include:
- FAIR data management, including best practices, ingestion, archival and data sharing
- Beginner and intermediate data analysis in R
- Electronic data capture
- Power analysis for research studies
Contact
Data management
We offer support in managing translational medicine datasets, including extract-transform-load operations, provenance, archiving, and transfer between partners. Our expertise involves data protection impact assessment, developing a data management plan, and supporting FAIR principles in your project.
| Service | Scope | Topic | Contact |
|---|---|---|---|
| Support for NCER-PD cohort | LCSB and Luxembourg-wide | Clinical and omics data Translational medicine | Venkata Satagopam |
| Support for translational medicine data via ELIXIR-LU | LCSB, Worlwide | Clinical and omics data Translational medicine | Reinhard Schneider |
| Daisy | LCSB, ELIXIR-LU | Data management platform Translational medicine | Valentin Grouès |
| LCSB File Transfer (LFT) | LCSB | Data transfer Sensitive data | Valentin Grouès |
| Project | Scope | Topic | Contact |
|---|---|---|---|
| ELIXIR-CONVERGE | LCSB, Worldwide | Standardisation of life science data management | Venkata Satagopam |
| Smart4Health | Worldwide | Citizen-centred EHR exchange for personalized health | Venkata Satagopam |
| FAIRplus | Worldwide | Tools, guidelines for making life science data FAIR | Venkata Satagopam |
Software development
We offer help in development of custom bioinformatics applications. Our expertise involves building web services for computational workflows, tools for complex data visual exploration and analytics, or platforms supporting text-mining knowledge. We develop catalogue services, like the catalogue of ELIXIR-LU datasets, or a database indexing LCSB publications.
| Service | Scope | Topic | Contact |
|---|---|---|---|
| BioKB | LCSB, Worldwide | Valentin Grouès | |
| PAWS | LCSB | Valentin Grouès | |
| Pisquared | LCSB | Valentin Grouès | |
| Data catalog | LCSB, ELIXIR-LU | Valentin Grouès | |
| SMASCH | LCSB, Worldwide | Valentin Grouès | |
| ADEPT | LCSB, Worldwide | Sascha Herzinger |
| Projects | Scope | Topic | Contact |
|---|---|---|---|
| HealthyCloud | Worldwide | ||
| IDERHA | Worldwide | Venkata Satagopam |
Research IT infrastructure
The LCSB sysadmins team supports the research IT infrastructure of the LCSB, helping with both day-to-day activities and computationally demanding and data-heavy tasks. We develop and maintain the hardware systems for data storage and computational workflows, and manage software and services essential for data sharing and code development.
We offer services targeted at all researchers at the LCSB (focus “Research” in the table below), some more specialised services for computational researchers (“code management”, “data analysis”, “data science”), and we maintain the infrastructure that supports these services in the background (“IT infrastructure support”).
| Service | Focus | Description | Contact |
|---|---|---|---|
| Software license management | Research | Handling licensed software supporting LCSB research | Sarah Peter |
| Lab IT | Research | Support for software, services and computational hardware needed for wetlab experiments | Noua Toukourou |
| Data sharing/exchange | Research | Reliable and secure data exchange within LCSB and outside | Sarah Peter |
| Hardware acquisition, setup & maintenance | IT infrastructure support | Providing computational resources for LCSB data analysis and modelling | Sarah Peter |
| Virtual machines | IT infrastructure support | Setup and maintenance of computing environments for workflows and (web) services | Sarah Peter |
| Backups | IT infrastructure support | Handling backups for LCSB data, computational workflows, and services | Sarah Peter |
| User management | IT infrastructure support | Handling users of shared services provided by the Bioinformatics Core | Sarah Peter |
| Software | Focus | Description | Contact |
|---|---|---|---|
| Owncloud | Research | LCSB cloud file storage | Noua Toukourou |
| GitLab | Code management | A platform for code versioning and sharing | Sarah Peter |
| RStudio server | Data analysis Data science | Development of analytics workflows for R | Sarah Peter |
Request services
You can see and request some of our support catalogue on ServiceNow (LCSB IT category).
For any other support you can email us.