Open Bioinformatics Foundation (OBF)
Open Source & Open Science in biological research
- 45
- Projects
- 7
- Years accepted
- 5
- In 2022
Projects by year
452022
5 acceptedShow
Feature Viewer - Enhanced User Experience and Performance
Accepted project · by Chalith Tharuka
Analyzing positional features/annotations in sequences is important in bioinformatics. Visualizing such data is quite a challenging task, considering...
Migration of the backend to Express, GraphQL, and MongoDB
Accepted project · by Devesh Kumar
Currently, the backend of the journal policy tracker is on Flask and SQLite3. The goal for this project is to create a full-fledged functioning...
The project aims at helping researchers find journals that require open source code easily. I aim to create a user interface that could seamlessly...
Efficient data layout for mass spectrometry data (OpenMS)
Accepted project · by Pranav Joshi
In this project, we need to implement a zero-cost abstraction using Modern C++, which can help us to switch between Structure of Arrays (SoA) and...
Genstorian data refinement tool is pipeline to identify allele names in genotype of a model organism and strain information related to the allele...
2021
8 acceptedShow
This project aims to add portable implementations for SIMD ISA extension AVX-512 functions which are not yet supported by SIMDe. This will make...
Developing WellcomeML further for the visualisation of academic research data
Accepted project · by Federica Trevisan
Synopsis WellcomeML is a python package containing a set of utility functions that use machine learning for reading, processing, embedding and...
Enabling and prototyping JavaScript visualizations in the Qt-based viewer TOPPView (OpenMS).
Accepted project · by Dhanmoni Nath
This project aims to enable JavaScript visualizations in TOPPView using Qt WebEngine and its different modules.
The aim on this project is to implement NEON functions into SIMD which are not yet supported. Adding these implementations will allow the NEON SIMD...
Design and implementation of Code is Science front-end using ReactJS
Accepted project · by Isaac Miti
The Code is science website is currently built using vanilla HTML, CSS and JavaScript with Ruby as part of its backend. The current frontend needs to...
Data streaming in scientific workflows, implementation for Toil
Accepted project · by Mihai Popescu
Toil is an open-source Python workflow engine that lets people write data analysis pipelines in Python, CWL, and WDL. Toil has support for common...
gtfBase- A curated resource of multispecies genomic regions
Accepted project · by Tanishq Gupta
While GTF files are by themselves comprehensive, a lot of analysis is focused on individual features. For example, any analysis focused on...
Development of a user interface to visualise VEP data using neXtProt tools
Accepted project · by Shrey Sachdeva
The goal of this project would be to develop a web based user interface to visualise the variant prediction data from VEP plugin using the neXtProt...
2020
8 acceptedShow
- Implementation of SVML in SIMDeHimanshi Mathur
- OpenMS R-PackageShekhar Shukla
- Parallel Graph Traversal for Variation GraphsFrancesco Porto
- Implementing user-friendly search featuresBoshen Yan
- Healthcare-Researcher-Connector (HRC): A Federated Learning package for bridging the gap between Healthcare providers and researchersSrijan Verma
- SIMDe : Add implementations of ISA extensions (SSE4.2 and AVX512) and NEON implementations of SSE4.1,SSE4.2,SSE3,SSSE3 ISA extensionHidayat Ullah Khan
- Protein sequence and structural analysis CWL pipeline for comparative biologyEliza Martin
- Using DeNovo Sequencing to Predict Protein Database SuitabilityT. Waschischeck
2019
5 acceptedShow
2018
5 acceptedShow
- Adding methods to cobrapy for improved constraint-based metabolic modelling.synchon
- Frontend Website Student Project for BioJSSarthak Sehgal
- Implement the support for Research Object specification into Nextflow frameworkEdgar Garriga Nogales
- Improve Posterior Error Probability Estimation For Peptide Search Engine ResultsSophia Mersmann
- Backend Website Student ProjectMEGH THAKKAR
2017
7 acceptedShow
- Adding Python 3 compatibility and improving mypy support for cwltoolManvendra Singh
- Implement algorithms for the generation of high-resolution isotope patternsNikos Patikas
- antiSMASH Migration to Template SystemMariana Nave
- ETE/Tree matcherDimitris Pliakos
- GeneNetwork Genome BrowserChristian Fischer
- Common Workflow Language reference implementation modernization- Making cwltool and schema-salad, Microsoft Windows compatible and providing complete Python 3 support for cwltool and schema-saladKapil kumar
- Bionode-Watermill - A Streaming Workflow Engine for BioinformaticsTiago Jesus
2016
7 acceptedShow
- openSNP: Linking Phenotypes to SNPs in openSNPVivek Rai
- Bionode workflow engine for streamed data analysisthejmazz
- openSNP: Extending Quantified-Self Support in openSNPgdyer
- Automated tool wrapper/converter for CWLAnton Khodak
- OpenSNPmateusjabour
- Improve the prediction for RiPP clustersMNave
- GeneNetwork Genome Browserchristian_f
Public proposals
2- GtfBase2021 · Tanishq Gupta · Status not recorded · from saketkc/fos-proposals
- Linking_Phenotypes_with_SNP2016 · Vivek Rai · Accepted · from saketkc/fos-proposals
Read them for structure, not to copy. All proposals for Open Bioinformatics Foundation (OBF).
