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Life Science/Bioinformatics Workshop

16 January 2023
Online
Europe/Berlin timezone

Martin Leandro Paleico

Contribution List

12 out of 12 displayed
  1. 5. Welcome and Motivation
    Julian Kunkel, Martin Leandro Paleico (GWDG)
    16/01/2023, 14:00

    Introduction and motivation/goals for this workshop

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  2. 1. Current Bioinformatics Services
    Martin Leandro Paleico (GWDG)
    16/01/2023, 14:15

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

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  3. 14. Stefanie Mühlhausen/Pavan Siligam (GWDG): Alphafold on the SCC: An application of software containers in HPC
    16/01/2023, 14:30

    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.

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  4. 16. Andreas Leha: RShiny applications support semi-automatic workflows
    16/01/2023, 14:45

    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.

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  5. 13. Hendrik Nolte (GWDG): SecureHPC: A Secure Partition to Process Sensitive Data on a Shared HPC System
    16/01/2023, 15:00

    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.

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  6. 11. Martin Schulte-Rüther: R-based machine learning models as an autism detection tool
    16/01/2023, 15:15

    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.

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  7. 12. Carsten Fortmann-Grote: RAREFAN: A publicly accessible bioinformatic pipeline on a cloud server - Implementation and limitations
    16/01/2023, 15:30

    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...

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  8. 10. Jonaid Hossain: The DANCE Framework
    16/01/2023, 15:45

    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.

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  9. 15. RShiny at the GWDG: Showcase (If time is available/replacement)
    Martin Leandro Paleico (GWDG)
    16/01/2023, 15:45
  10. 17. Manolis Bastakis: Employing high-performance computing services from GWDG to discover new gene regulatory networks in fungi
    16/01/2023, 16:00

    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...

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  11. 3. Discussion
    Martin Leandro Paleico (GWDG)
    16/01/2023, 16:30

    Discussion of the user presentations

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  12. 4. Conclusions
    Martin Leandro Paleico (GWDG)
    16/01/2023, 17:00

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

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