🎊 Welcome to MENA Biohackathon Contributors

[BatoolMM]

Description of feature

🎊 Welcome to MENA Biohackathon Contributors! We're excited that you're here 🎉

This ticket will serve as the central point tracking the contributions of perspective MENA Biohackathon Contributions.

This project will create NextFlow workflow and documentation that support RTL languages and non-Latin scripts. NextFlow is a powerful and flexible workflow language that enables the development of portable and reproducible workflows and simplifies writing and deploying data-intensive computational pipelines on any infrastructure. The nf-core community uses NetFlow to develop highly optimised, portable, documented and easy-to-use workflows pipelines and templates. However, all of the current nf-core pipelines were developed for NGS data and none was developed for structural biology or molecular dynamics workflows (MD). This project will introduce a new workflow for molecular dynamics (MD) simulations which are important tools for understanding the physical basis of the structure and function of biological macromolecules. The workflow will use different tools, including gromacs, gmx_MMPBSA, HeroMDAnalysis, VMD, MDTraj and others.

The output of this project can be divided into 2 parts:

• Developing a workflow for protein Molecular Dynamics simulations. In order to produce tangible outcomes within the tight timeframe, we will exclude non-protein systems in the prototype of the workflow. This will be the 1st nf-core workflow that applies NextFlow to study protein dynamics.

• Implementing new functionality to support the documentation in RTL using a non-Latin script such as Arabic. In order to encourage the broad uses of this workflow and NextFlow in the MENA region, all the documentation will be provided in both Arabic and English. However, the nf-core template doesn’t yet support documentation in non-latin script or RTL languages. We will introduce a new feature in the nf-core to enable this new functionality. This will not just be applied in the Molecular Dynamics workflow pipeline but will also make nf-core (in general) more usable by non-English communities towards broader internationalisation of open source tools.

How to start?

• GitHub
  If you know refresher about git/GitHub, please watch this video.
• Molecular Dynamics for Proteins
  This is the famous tutorial by Lemkul's Lab to guide a new user through the process of setting up a simulation system containing a protein (lysozyme) in a box of water, with ions. Each step will contain an explanation of input and output, using typical settings for general use.
• NextFlow and nf-core
  • This training will guide you through the use of NextFlow and nf-core.
  • This video shows you how to work with GitHub using VSCode and Github CLI
  • This video go through the brand-new nf-core subworkflows!
  • This video explain how to use nf-core components despite it being outside the main nf-core organisation
  • This video explain what the perfect DSL2 coding style should be.
  • This video go through the latest changes to the DSL2 template

Communication

• Join nf-core Slack
• GitHub boards