GSoC Ideas 2021
Guidelines
Open Chemistry is an umbrella for projects in chemistry, materials science, biochemistry, and related areas. While we have participated in the last few Google Summer of Code programs and will apply again in 2021, there is no guarantee that we will be selected again for GSoC in 2021.
One important factor is that GSoC in 2021 will focus on shorter projects. You should consider the shorter timeline in your proposal.
We have gathered a pool of interested mentors together who are seasoned developers in each of these projects. We welcome original ideas in addition to what's listed here - please suggest something interesting for open source chemistry!
Adding Ideas
When adding a new idea to this page, please try to include the following information:
- A brief explanation of the idea.
- Expected results/feature additions.
- Any prerequisites for working on the project.
- Links to any further information, discussions, bug reports etc.
- Any special mailing lists if not the standard mailing list for the project
- Your name and email address for contact (if willing to mentor, or nominated mentor).
Proposal Guidelines
Students need to write and submit a proposal, we have added the applying to GSoC page to help guide our students on what we would like to see in those proposals.
Avogadro 2 Project Ideas
Avogadro 2 is a chemical editor and visualization application, it is also a set of reusable software libraries written in C++ using principles of modularity for maximum reuse. We offer permissively licensed, open source, cross platform software components in the Avogadro 2 libraries, along with an end-user application with full source code, and binaries.
Project: Python-based Compute and Data Server
Brief explanation: Avogadro would be more powerful with a local compute and data server
Expected results: A number of projects have build servers for larger projects that can also do compute, Jupyter, etc. Python has a number of lightweight data server frameworks such as FastAPI where RESTful APIs can be developed rapidly. Using this as a basis along with PostgreSQL, EdgeDB, or other database technologies the project would build a lightweight data layer for storing, searching, and visualizing data. Ideally this would be packaged in a container, and deployable to the cloud or run locally via pip or conda. A stretch goal would be to implement simple queuing and execution of jobs within the server API reusing Python projects to handle queuing, execution, etc.
Prerequisites: Experience in Python, some experience with C++/Qt and RESTful APIs.
Mentor: Marcus D. Hanwell (mhanwell at bnl.gov)
Project: Biological Data Visualization
Brief explanation: Efficient biomolecular visualization, including surfaces, cartoons, etc. would be ideal
Expected results: Support for residues, and reading secondary structure (e.g., PDB format) is now present. Additional rendering modes for secondary biological structures (i.e. ribbons, cartoons, etc.), building up a biomolecule from residues, and adding residue labels are desired. Code and algorithms may be adapted from 3DMol.js. Since biological molecules are often large (10^3 to 10^6 atoms and bonds), such implementations should be highly efficient and optimized, adopting symmetry and other techniques to improve interactivity and rendering performance. General extension of Avogadro for editing/interacting with biological data structures, and/or structures with named fragments would be ideal. Extending that to porting builders for fragment based building blocks would be a big plus once basic support for rendering is in place.
Prerequisites: Experience in C++, some experience with OpenGL and biochemistry ideally, but not necessary.
Mentor: Marcus D. Hanwell (mhanwell at bnl.gov) or Geoffrey Hutchison (geoffh at pitt.edu)
Project: Scripting Bindings
Brief explanation: Implement an embedded scripting language (i.e., Python) in Avogadro 2
'Expected results:’ Enable an embedded scripting console as well as support for implementing modular extensions (tools, rendering, etc.) in Python. Python bindings exist, using PyBind11 with the new codebase, and the Avogadro 2 core libraries are pip installable. Extending the coverage of the API from the rudimentary parts of core/io would be a good starting point. An ideal solution would connect to PySide2, to allow scripting to add UI like menu items, windows, etc. and provide documentation and example scripts. The interface should be maintainable as new classes and methods are added.
Example scripts, documentation, are highly encouraged.
Prerequisites: Experience in C++ and Python, some experience with PyBind11, Qt for Python, PySide suggested.
Mentor: Geoff Hutchison (geoffh at pitt dot edu) or Marcus D. Hanwell (mhanwell at bnl dot gov)
Project: Integrate with RDKit
Brief explanation: Integrate the RDKit toolkit into Avogadro for conformer sampling and force field optimization
Expected results: RDKit is a BSD-licensed cheminformatics toolkit with a wide range of features useful for Avogadro 2. Most notably, RDKit offers efficient and accurate 3D coordinate generation, conformer sampling, and force field optimization. Implement a connection between Avogadro objects (molecules and atoms) and RDKit objects and implement conformer sampling and force field optimization code.
'Prerequisites: Experience in C++, some experience with Python will be helpful.
Mentor: Geoff Hutchison (geoffh at pitt dot edu)
Project: Tools for Interactive Molecular Dynamics
Brief explanation: Building solvent boxes, implementing standard molecular dynamics using in-progress optimization framework.
Expected results: Avogadro (v1) has interactive force field optimization allowing building and manipulation (e.g., push-pull atoms into position). Some users call this 'video game mode' ;-) A new optimization framework is in progress, including calling external programs for energies and forces. The project would enable building out MD simulations, including tools to add water or solvent boxes, build larger systems (e.g., via PackMol integration) and implement simple MD integration and thermostats.
'Prerequisites: Experience in C++, ideally with knowledge of molecular dynamics methods and tools. Some Python would be helpful
Mentor: Geoff Hutchison (geoffh at pitt dot edu)
Open Babel Project Ideas
Open Babel is an open toolbox for chemistry, designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
Project: Integrate CoordGen library
Expected results: Schrodinger has released a BSD-licensed library for 2D chemical structure layout (https://github.com/schrodinger/coordgenlibs) and it has been successfully integrated into RDKit. The student will be responsible for integrating CoordGen into Open Babel. Code will be written in C++.
Mentor: Geoff Hutchison (geoffh at pitt dot edu)
Project: Implement MMTF format
Brief explanation: Implementation of MMTF file format in OpenBabel.
Expected results:' Macromolecular Transmission Format (MMTF) is a new compact binary format to transmit and store biomolecular structural data quickly and accurately (http://mmtf.rcsb.org). Your task is to implement support for this format in the OpenBabel open-source cheminformatics toolkit (http://openbabel.org). Code will be written in C++.
Mentor: Geoff Hutchison (geoffh at pitt dot edu) or David Koes (dkoes at pitt dot edu)
Project: Test Framework Overhaul
Brief explanation: Automated testing is an important part of maintaining code quality. This project will improve the current testing regime of openbabel.
Expected results: A comprehensive test framework that automates the generation of unit tests for all supported languages and simplifies the creation of new test cases will be implemented. The student will be responsible for choosing the most appropriate framework, porting existing test cases, and expanding the test suite to enhance code coverage.
Prerequisites: Experience in C++. Knowledge of modern software engineering practices or test frameworks is ideal.
Mentor: Geoff Hutchison (geoffh at pitt dot edu), David Koes (dkoes at pitt dot edu), the OpenBabel development community.
Project: Develop a JavaScript version of Open Babel
Brief explanation: Building on existing work, you will use Emscripten to compile the C++ codebase of Open Babel to JavaScript. This will make it easy to write in-browser applications that need cheminformatics functionality.
Expected results: Following from work described in a recent paper (https://pubs.acs.org/doi/abs/10.1021/acs.jcim.7b00434), a JavaScript version of the Open Babel toolkit will be created. The generation of any necessary wrappers should be automated to allow it to track changes in the Open Babel API.
Ideally, the project will adapt a core JavaScript library openbabel.js that allows modules, such as file formats to be imported separately (e.g., smilesformat.js, pdbformat.js, xyzformat.js, etc.)
Prerequisities: Some experience in C++, and also with JavaScript.
Mentor: Noel O'Boyle (baoilleach at gmail dot com)
Project: Develop a validation and standardization filter
Brief explanation: Given a particular molecular structure, can we say how chemically plausible is it, and use this as to filter or warn about problems (e.g., undefined stereo centers)?
Expected results: Given a set of reference structures (e.g. ChEMBL), it should be possible to build a model that can say how normal/unusual a query structure is. For example, given a set of drug-like molecules, a molecule with a ruthenium atom might be considered unusual; or given any set of molecules, a 5-coordinate carbon is unusual.
Such a model could be used as a filter, or as a warning to flag up problematic structures.
Code could be modeled on MolVS using RDKit [[1]]
Prerequisites: Experience in C++ or Python, and an interest in data science or statistics.
Mentor: Noel O'Boyle (baoilleach at gmail dot com) or Geoff Hutchison (geoffh at pitt dot edu)
cclib Project Ideas
cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. The goals of cclib are centered around the reuse of data obtained from these programs when stored in program-specific output files.
Project: Support for QCSchema JSON output
Bried explanation: The library already allows importing and exporting data between several formats. The QCSchema is a new JSON format that tries to standardize the way computational chemistry data is written and shared, so supporting the effort can be useful.
Expected results: Implement JSON output that conforms to the conventions of the MolSSI QCSchema.
Suggested readings:
- This cclib issue and the references there.
Prerequisites: Experience with Python, some experience with physics and chemistry also recommended.
Mentor: Eric Berquist (eric.john.berquist at gmail dot com) and/or Karol Langner (karol.langner at gmail dot com)
Project: Advanced Analysis of Quantum Chemistry Data
Brief explanation: The current cclib library offers some calculation methods, including fragment analysis and some charge models. Many modern analysis techniques exist to partition electron density, including computing gradients, Laplacians, ELF (electron localization function), Bader's AIM analysis, etc. Similarly, multiple partial charge assignment methods exist and can be implemented, including DDEC6.
Expected results: Implement additional analysis and quantum calculation methods, such as ELF (electron localization function), AIM (Bader's Atoms-in-Molecules) techniques, and/or DDEC6 atomic charges, with examples and tests.
Suggested Readings:
Prerequisites: Experience with Python and linear algebra (including numpy, scipy), some experience with numerical methods suggested.
Mentor: Geoff Hutchison (geoffh at pitt dot edu) and/or Karol Langner (karol.langner at gmail dot com)
Project: Implement new parsers
Brief explanation: There are outstanding issues on GitHub for supporting more programs, and parsing binary files for various QM programs (e.g. Gaussian, NWChem, and ORCA).
Expected results: Generate test data and unit tests, and implement new parsers.
Prerequisites: Experience with Python, and ideally familiarity with computational chemistry programs.
Mentor: Adam Tenderholt (atenderholt at gmail dot com) and/or Karol Langner (karol.langner at gmail dot com)
Project: Discovering computational chemistry content online
Brief explanation: There are tens or hundreds of thousands of computational chemistry results available online - let's mine them!
Expected results: Build a crawler that identifies and indexes computational chemistry logfiles online, and provides the ability to extract the data they contain with cclib.
Prerequisites: Experience with Python, and ideally familiarity with computational chemistry and web indexing.
Mentor: Karol Langner (karol.langner at gmail dot com)
3Dmol.js Project Ideas
3Dmol.js is a modern, object-oriented JavaScript library for visualizing molecular data that is forked from GLmol. A particular emphasis is placed on performance.
Project: Improve 3Dmol.js
Brief explanation: Make significant improvements to 3Dmol.js functionality or performance.
Expected results: This is an open-ended project that must be driven by the applicant. A strong proposal will identify significant shortcomings in the current code and explain how it will be addressed. The GitHub Issues page may provide some ideas. A proposal must include a significant initial pull request.
Prerequisites: Experience with JavaScript and client-server programming, some experience with OpenGL/WebGL ideal, but not necessary.
Mentor: David Koes l (dkoes@pitt.edu)
gnina Project Ideas
gnina is a C/C++ framework for applying deep learning to molecular docking.
Project: Improve gnina
Brief explanation: Make significant improvements to gnina functionality or performance.
Expected results: This is an open-ended project that must be driven by the applicant. A strong proposal will identify significant shortcomings in the current code and explain how it will be addressed. The GitHub Issues page may provide some ideas. A proposal must include a significant initial pull request.
Prerequisites: Experience with CUDA/C/C++ programming and the basics of deep learning.
Mentor: David Koes l (dkoes@pitt.edu)
NWChem Project Ideas
NWChem is widely used open-source computational chemistry software ([2]) that tackles a wide variety of scientific problems.
Project NWChem-JSON
Brief explanation: Expansion of JSON capabilities in NWChem to plane wave DFT dynamics and molecular dynamics.
Expected results: Expanding JSON output generator in the NWChem source to include plane wave DFT dynamics and classical molecular dynamics capabilities. In addition the "Python NWChem output to JSON converter" needs to be expanded to include these capabilities. The latter strongly overlaps with cclib's project ideas for building a complete set of Python parsers. Questions as to handle large data structures in conjunction with JSON need to be addressed.
Prerequisites: Experience with Fortran90 and Python
Mentor: Bert de Jong (wadejong at lbl dot gov)
Project NWChem-Python-Jupyter Interface
Brief explanation: Exposing and binding NWChem data structures and computational APIs to Python and utilize those in Jupyter notebooks
Expected results: NWChem currently has a very limited interface with Python. But, more and more developers are using platforms such as Python to sandbox new theories, methods and algorithms. In addition, the extended Python interface could be integrated into a Jupyter notebook. A full Python interface needs to be developed for the NWChem software suite.
Prerequisites: Experience with Fortran and Python
Mentor: Bert de Jong (wadejong at lbl dot gov)
JSON-LD for Chemical Data
Brief explanation: Transforming NWChem and Chemical JSON formats to JSON-LD
Expected results: Refactoring NWChem JSON and Chemical JSON formats to utilize JSON-LD. Currently the JSON documents that are created are single dense objects, even though they could be handled as linked objects. This transformation will enable the generated computational data and objects to be more naturally aligned with triple-stores and knowledge graphs when connecting with experimental data.
Prerequisites: Experience with Python and JSON-LD
Mentor: Bert de Jong (wadejong at lbl dot gov)
DeepChem Project Ideas
DeepChem aims to provide a high quality open-source toolchain that democratizes the use of deep-learning in drug discovery, materials science, quantum chemistry, and biology. Additional project ideas are discussed at https://forum.deepchem.io/t/google-summer-of-code-ideas/356.
Project: DeepChem Jax Support
Brief explanation: Build infrastructure in DeepChem to support models implemented in Jax.
Expected results: DeepChem currently doesn’t have a good way to build models with Jax. This project would work to add a wrapper JaxModel in the style of KerasModel and TorchModel that allows for convenient wrapping of arbitrary Jax models in DeepChem. The project will involve implementing JaxModel, writing a suitable test suite, and putting together a good tutorial on how to use Jax with DeepChem as a jupyter notebook.
Prerequisites: Jax, Python
Mentor: Bharath Ramsundar (bharath at deepforestsci dot com)
Project: PyTorch Lightning Implementation
Brief explanation: Allow for implementation of DeepChem models in PyTorch Lightning.
Expected results: PyTorch lightning is a popular framework for PyTorch. This project would look into enabling the easy construction of PyTorch lightning based models for DeepChem. Completion of this project should require the implementation of a good test suite and a jupyter notebook tutorial for implementing PyTorch Lightning models in DeepChem.
Prerequisites: PyTorch Lightning, Python
Mentor: Bharath Ramsundar (bharath at deepforestsci dot com)
Project: Semiconductor Modeling Support
Brief explanation: Add support for semiconductor modeling deep learning tools.
Expected results: This project would involve implementing semiconductor models from https://arxiv.org/ftp/arxiv/papers/2101/2101.04383.pdf. These models should be added to DeepChem along with suitable tests, and a suitable jupyter notebook usage tutorial.
Prerequisites: PyTorch/TensorFlow, Python
Mentor: Bharath Ramsundar (bharath at deepforestsci dot com)
Project: Protein Language Models
Brief explanation: Add support for protein language models.
Expected results: This project would implement a language model for protein sequence modeling, using a transformer or suitable language model on a dataset like UniProt. Models should be added to DeepChem along with suitable tests and a good jupyter notebook usage tutorial.
Prerequisites: PyTorch/TensorFlow, Python
Mentor: Bharath Ramsundar (bharath at deepforestsci dot com)
Miscellaneous Project Ideas
These ideas would likely benefit two or more projects.
Project: OneMol: Google Docs & YouTube for Molecules
Brief explanation: There is a huge need in the research community for improved collaboration tools on web and desktop. OneMol will provide an open API for collaborating on molecular data that both Avogadro and 3Dmol.js will support as reference implementations. OneMol compliant applications will be able to manipulate and view molecular data in real time so that changes made by one client will be propagated to other clients.
File-sharing is a means for sharing data, but it does not share real-time interactions; each user’s data exists in its own isolated environment. Screen-sharing provides a common viewpoint for all participants, but allowing others to interact with the data requires granting access to the host workstation. This approach is needlessly inefficient for the task of collaborating on molecular data, and this inefficiency introduces scalability issues. For example, a simple rotation necessitates a full screen update when the fundamental change in state was a simple change in viewing angles.
The OneMol framework consists of three main components: a client module, embedded in a molecular viewer; a facilitator module that enforces a consistent viewer state between all the clients; and a storage module that stores the raw molecular data. All three modules may coexist on the same machine within the same application. However, we anticipate a more common modality will be to use a publicly hosted facilitator server, since this simplifies network connectivity in the face of firewalls and network address translation.
Expected results: Prototype web services to allow web and/or desktop collaboration using 3DMol as a viewer, likely integrating with existing storage systems (e.g., MongoChem or PQR).
Prerequisites: Experience with scripting, and web services. Interest and experience with databases like MongoDB or DSpace very helpful.
Mentor: David Koes (dkoes@pitt.edu) or Geoffrey Hutchison (geoffh at pitt.edu)