This BioExcel interest group is for users (and potential users) of Scientific Workflow systems for data analysis and pipe-lining of biomolecular simulation and modelling tools; in particular using Galaxy, Apache Taverna, KNIME, COMPSs and Common Workflow Language.
Covering pros and cons of these workflow systems, practical workflow design and setup, discussion in this group also covers deployment questions on HPC/cloud infrastructure, like the use of Docker or Singularity for packaging command line codes.
To receive occasional updates on workflows-related activities, feel free to sign up for the BioExcel interest group Workflows.
- 2018-02-15: BioExcel Workflows IG newsletter #4
- 2017-10-10: BioExcel Workflows IG newsletter #3
- 2017-07-17: BioExcel Workflows IG newsletter #2
- 2017-06-12: BioExcel Workflows IG newsletter #1
Anyone can ask questions on BioExcel’s support forum (ask.bioexcel.eu) about building workflows, deciding on workflow systems, integrating workflows with the BioExcel core tools (CPMD, HADDOCK, GROMACS), how to run workflows on computational resources (grid, cloud, HPC). Subscribe to the Workflows IG category to follow relevant discussions, contribute and post your own questions.
For a more informal approach, feel free to join the Workflows chat room on Gitter – Gitter is semi-asynchronous so you can come back later or be notified by email for replies.
Webinars and slides
Below are some of the BioExcel webinars that focus on workflows (any bold dates indicates upcoming webinars):
- 2018-11-07: COMPSs: a high level framework for the development of parallel applications
- 2018-06-27: BioSimSpace – filling the gaps between molecular simulation codes
- 2018-02-28: CWLEXEC, A new open source tool to run CWL workflows on LSF
- 2017-10-11: MDStudio, microservice based molecular dynamics workflows
- 2017-07-17: BioExcel and OpenPHACTS: Building pharmacological workflow blocks for virtual screening
- 2017-06-21: Introduction to the Common Workflow Language (CWL) project
- 2016-11-16: Large-scale analytical workflows on the cloud using Galaxy and Globus
To be informed of upcoming BioExcel webinars, sign up for the BioExcel newsletter.
Here are some other webinars from/with our collaborators which may also be of interest to the BioExcel Workflows interest group:
- 2017-11-13: The transfer of large volume, electronic, confidential, human data (ELIXIR Webinar) [video]
- 2017-04-20: Workflow tools for Life Science Research (Open PHACTS webinar) [video, slides]
- 2017-03-15: Bioconda and BioContainers (ELIXIR Webinar) [video]
- 2016-07-28: Loading data into Open PHACTS (Open PHACTS webinar) [video, slides]
- 2016-07-06: Open PHACTS Architecture and Docker Install (Big Data Europe webinar on Open PHACTS pilot) [video, slides]
- 2016-05-18: Make research reproducible again (ELIXIR hackathon) [slides]
- 2016-04-21: Leveraging integrated pharmacological datasets for cross-domain queries (former BioExcel Use Case) [slides]
BioExcel Workflow Publications
- Workflows for Science: a Challenge when Facing the Convergence of HPC and Big Data (10.14529/jsfi170102)
- Dynamic energy-aware scheduling for parallel task-based application in cloud computing (10.1016/j.future.2016.06.029)
- Enabling Precision Medicine via standard communication of NGS provenance, analysis, and results (10.1101/191783)
- Robust cross-platform workflows: how technical and scientific communities collaborate to develop, test and share best practices for data analysis (10.1007/s41019-017-0050-4)
- Copernicus, a hybrid dataflow and peer-to-peer scientific computing platform for efficient largescale ensemble sampling (10.1016/j.future.2016.11.004)
- I’ll take that to go: Big Data bags and minimal identifiers for exchange of large, complex datasets (10.1109/BigData.2016.7840618)
- BioExcel Deliverable 2.1 – State of the art and gap analysis (10.5281/zenodo.263963)
- BioExcel Deliverable 2.2 – First Release of Workflow Blocks and Portals (10.5281/zenodo.263965)