Life Science/Bioinformatics Workshop

Contribution List

5. Welcome and Motivation

Julian Kunkel, Martin Leandro Paleico (GWDG)

1/16/23, 2:00 PM

Introduction and motivation/goals for this workshop

1. Current Bioinformatics Services

Martin Leandro Paleico (GWDG)

1/16/23, 2:15 PM

Short presentation of the bioinformatic services services currently offered at the GWDG

14. Stefanie Mühlhausen/Pavan Siligam (GWDG): Alphafold on the SCC: An application of software containers in HPC

1/16/23, 2:30 PM

Presentations

Alphafold is a recent popular tool for predictive protein folding. Due to its nature, it is a rather complex tool to install. For this reason, it benefits from the consistent and repeatable deployment made possible by container technology. An example from our own SCC.

16. Andreas Leha: RShiny applications support semi-automatic workflows

1/16/23, 2:45 PM

Presentations

This is a project of the "Scientific Core Facility
Medical Biometry and Statistical Bioinformatics" where we designed a shiny app that our user then could use to fine-tune our analyses for their data.

13. Hendrik Nolte (GWDG): SecureHPC: A Secure Partition to Process Sensitive Data on a Shared HPC System

1/16/23, 3:00 PM

Presentations

Privacy and security concerns play an increasingly important role when dealing with medical and other types of sensitive data common in the life sciences. How can safety be ensured when also needing to process data off-site? An example from our own HPC services.

11. Martin Schulte-Rüther: R-based machine learning models as an autism detection tool

1/16/23, 3:15 PM

Presentations

R_based machine learning models were trained on the GWDGs HPC services. These models aim to improve a diagnostic tool for autism. Rshiny was used to showcase the models in a webapp (https://msrlab.shinyapps.io/asd-ml-jcpp/). The webapp saves data to a postgresql server also provided by the GWDG.

12. Carsten Fortmann-Grote: RAREFAN: A publicly accessible bioinformatic pipeline on a cloud server - Implementation and limitations

1/16/23, 3:30 PM

Presentations

In this presentation I will briefly describe the functionality and modular implementation of our RAREFAN web service, an online tool
to find and analyse REPINs and RAYTs [1]. RAREFAN runs ontop the python flask framework and uses the redis queuing system to schedule jobs and manage task dependencies on a GWDG hosted cloud server. It drives a bioinformatic pipeline consisting of various self...

10. Jonaid Hossain: The DANCE Framework

1/16/23, 3:45 PM

Presentations

DANCE (https://omicsml.ai/) is a PyTorch-based deep learning toolbox designed for single cell analysis. The goal of this framework is to help develop personalized deep learning models for analyzing single-cell data at scale.

15. RShiny at the GWDG: Showcase (If time is available/replacement)

Martin Leandro Paleico (GWDG)

1/16/23, 3:45 PM

Presentations

17. Manolis Bastakis: Employing high-performance computing services from GWDG to discover new gene regulatory networks in fungi

1/16/23, 4:00 PM

Presentations

It has been speculated that earth hosts ca. 1.5 million species of fungi. These organisms show great variety regarding their forms, living environments, and their interactions with other organisms as well. The implications of fungi in our health, industry, and in our economy, are being enormous for centuries; becoming even more prominent year by year. Therefore, it can be easily postulated...

3. Discussion

Martin Leandro Paleico (GWDG)

1/16/23, 4:30 PM

Discussion of the user presentations

4. Conclusions

Martin Leandro Paleico (GWDG)

1/16/23, 5:00 PM

Collaborative elaboration of a roadmap and goals list for bioinformatics at the GWDG in the coming year.

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