Mapping the OSS tool landscape

OSSci Interest Groups Map of Science
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Welcome to OSSci!

Please share any OSS projects that are essential for your work, tools you see are gaining traction in your field, or anything else that has recently popped up on your radar.

Please provide a link to the repo (e.g., GitHub) and any additional context that might be helpful for others to explore.

Thanks!

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My 2 cents:
A typical way of mapping software related to a specific topic on github is to create a “awesome list”. It seems there is already one here GitHub - Bluteshi/awesome-climate-research: A curated list of resources about various climate research topics that could help us getting started.

I use and sometimes contribute to the following (python) libraries:

Also the CF convention is a very important organization for standardization of climate and earth observation data: GitHub - cf-convention/discuss: A forum for proposing standard names; and any discussion about interpretation, clarification, and proposals for changes or extensions to the CF conventions.

Another community maintaining several tools is Pangeo: Pangeo · GitHub

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Excellent, thank you!

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Mining publications:

  • GORBID: an open source machine learning library, to convert thousands of open access publication PDFs into TEI/XML text
  • howisonlab/softcite: A gold-standard dataset of software mentions in research publications. Used to train GORBID to detect software mentions in publication body.

Interactive network visualizations in Jupyter Notebooks:

Turning Jupyter Notebooks into Web applications:

  • ScyPy23 tutorial: tutorial for creating web apps with Jupyter Notebooks (I wrote this tutorial)
  • Feel free to message me if this kind of thing seems interesting to you
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Adding on to aoun.abel’s comments above – I’m not a domain expert, but we used this “awesome list” repo: GitHub - protontypes/open-sustainable-technology: A curated list of open technology projects to sustain a stable climate, energy supply, biodiversity and natural resources. to get lists of sustainability-related software for ORCA (e.g. https://orca.eto.tech/?field_of_study=Renewable+Energy&order_by=stargazers_count&show_list=true).

I think we could share the paper-repo mappings from ORCA if that would be of interest, as well

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OSSci is attending the EuChemS CompChem 2023 conference in Thessaloniki, Greece this week. Around 300 attendees, mostly from Europe, are here to share their latest findings in computational chemistry.

We’re using this opportunity to hear which OSS tools are being used and collect data for our prototype. So far, seven tools have come up:

  • DeepMD-kit – A deep learning package for many-body potential energy representation and molecular dynamics: https://github.com/deepmodeling/deepmd-kit
  • OpenMolcas – A quantum chemistry software package developed by scientists and intended to be used by scientists. It includes programs to apply many different electronic structure methods to chemical systems, but its key feature is the multiconfigurational approach, with methods like CASSCF and CASPT2: https://gitlab.com/Molcas/OpenMolcas
  • TheoDORE – A package for Theoretical Density, Orbital Relaxation and Exciton analysis: https://theodore-qc.sourceforge.io/
  • plumed2 – The community-developed PLUgin for MolEcular Dynamics: https://github.com/plumed/plumed2
  • CP2K – A quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems: https://github.com/cp2k/cp2k
  • Quantum ESPRESSO – An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials: https://gitlab.com/QEF/q-e
  • iRASPA – This software is a general purpose classical simulation package. It has been developed at Northwestern University (Evanston, USA) during 2006-2011 in active collaboration with University Pablo de Olavide (Seville, Spain), and the Technical University of Delft. It can be used for the simulation of molecules in gases, fluids, zeolites, aluminosilicates, metal-organic frameworks, carbon nanotubes and external fields: https://github.com/iRASPA/RASPA2

By manually pulling the contributors from GitHub and GitLab, a first few connections between projects have appeared (via mutual contributors):

Screenshot 20230828 Kumu MOSS
Screenshot 20230828 Kumu MOSS1920Ă—990 75.7 KB

Hearing good feedback here so far. Hope to have a more complete view ready by this time Wednesday.

A few questions people are asking:

  • How can I contribute (e.g., to add content, flag errors)?
  • Will the map have the ability to filter tools by programming language?
  • Will there be some kind of rating system to help indicate the health of a project?

Follow along on Kumu (you can filter by tag “EuChemSCompChem” to show only the additions that were made during the conference): https://kumu.io/tbonnemann/ossci-moss#moss/moss-euchemscompchem

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Here’s a short write-up of this week’s mapping exercise in Greece: EuChemS CompChem: Mapping OSS in Computational Chemistry

Let us know what you think!