Feature Viewer - Enhanced User Experience and Performance
Contributor: Chalith Tharuka
Analyzing positional features/annotations in sequences is important in bioinformatics. Visualizing such data is quite a challenging task, considering...
Science and medicine
Open Bioinformatics Foundation (OBF)
Open Source & Open Science in biological research
Technologies
CC++CSSGitGitHubHTMLJavaScriptPythonReact
Topics
bioinformaticscomputational biologygenomicsopen scienceOpen Source Bioinformaticsworkflows
- Total projects
- 45
- Years participating
- 7
- Most recent
- 2022
Participation history
Historical projects
Migration of the backend to Express, GraphQL, and MongoDB
Contributor: 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...
Journal tracker – finalise and deploy React front-end
Contributor: Padmaja Bhol
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)
Contributor: 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...
Genestorian data refinement
Contributor: Anamika Yadav
Genstorian data refinement tool is pipeline to identify allele names in genotype of a model organism and strain information related to the allele...
Implementations of AVX-512 functions
Contributor: Kunwar Maheep Singh
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
Contributor: 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).
Contributor: Dhanmoni Nath
This project aims to enable JavaScript visualizations in TOPPView using Qt WebEngine and its different modules.
Implementation of NEON functions (SIMDe)
Contributor: Atharva Nimbalkar
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
Contributor: 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
Contributor: 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
Contributor: 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
Contributor: 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...
Implementation of SVML in SIMDe
Contributor: Himanshi Mathur
This project will be aimed to create an API-compatible open-source implementation of Intel's proprietary SVML which would be portable to other...
OpenMS R-Package
Contributor: Shekhar Shukla
OpenMS, an open-source C++ library for the analysis of mass spectrometric data exposes a large part of its functionality to the Python community via...
Parallel Graph Traversal for Variation Graphs
Contributor: Francesco Porto
Traditionally, Bioinformatics has focused its efforts on the study of single genomes, each representing an individual of a certain species. In more...
Implementing user-friendly search features
Contributor: Boshen Yan
Pysradb provides a convenient method to retrieve information from NCBI’s SRA database. Currently, pysradb is transitioning to phase out its...
Healthcare-Researcher-Connector (HRC): A Federated Learning package for bridging the gap between Healthcare providers and researchers
Contributor: Srijan Verma
Nowadays, sharing and use of human biomedical data is heavily restricted and regulated by multiple laws. Such data-sharing restrictions allow keeping...
SIMDe : Add implementations of ISA extensions (SSE4.2 and AVX512) and NEON implementations of SSE4.1,SSE4.2,SSE3,SSSE3 ISA extension
Contributor: Hidayat Ullah Khan
The project deals with writing portable implementations for SIMD ISA extensions SSE4.2 and AVX-512 functions and NEON implementations for...
Protein sequence and structural analysis CWL pipeline for comparative biology
Contributor: Eliza Martin
While there are a multitude of open source ML methods for prediction of various structural or biological related attributes, there are no open source...
Using DeNovo Sequencing to Predict Protein Database Suitability
Contributor: T. Waschischeck
When using mass spectrometry to analyze protein samples it is key to use the appropriate protein database. Most of the time a sample from only one...
antiSmash submission redesign
Contributor: Jeevan
antiSmash run multiple instances of the submission page, depending on whether people want to analyse bacterial or fungal sequences, or run the...
Add Variant Graph (VG) support to BioD
Contributor: Njagi Mwaniki
The current representation of reference genomes is as a sequence of nucleotides akin to a long string. Intuitively, this doesn’t represent a genome...
BAM to ADAM converter on Sambamba’s base
Contributor: Nick Rozinsky
This project is aimed to build an efficient BAM format to ADAM format converter utilizing Sambamba library base.
Interactive Yeoman generator for BioJS components
Contributor: Nikhil Vats
BioJS is a library of over one hundred JavaScript components enabling users to visualise and process data using current web technologies. BioJS makes...
Add blockchain and hyperledger support for the ‘Journal of Open Data Publications’
Contributor: Pradyumna Bang
Open science is a movement that promotes open access to research data, publications, and scientific collaboration. It promises to increase...
Adding methods to cobrapy for improved constraint-based metabolic modelling.
Contributor: synchon
Constraint-Based Reconstruction and Analysis (COBRA) methods for Genome-wide Metabolic Networks (GEMs) have proven to be essential for the varied...
Frontend Website Student Project for BioJS
Contributor: Sarthak Sehgal
BioJS is a library of over two hundred JavaScript components which enables users to visualise and process data. BioJS currently has two websites: ...
Implement the support for Research Object specification into Nextflow framework
Contributor: Edgar Garriga Nogales
The goal of this project is to implement the support for Research Object specification into Nextflow workflow framework, with the aim to improve the...
Improve Posterior Error Probability Estimation For Peptide Search Engine Results
Contributor: Sophia Mersmann
OpenMS is an open-source software C++ library for mass spectrometry (MS) data management and analyses. A common task in proteomics is to identify and...
Backend Website Student Project
Contributor: MEGH THAKKAR
BioJS is a library of over two hundred JavaScript components enabling developers to visualize and process data using current web technologies. The...
Adding Python 3 compatibility and improving mypy support for cwltool
Contributor: Manvendra Singh
The goal of this proposal is to enhance support and usability of cwltool by: Adding Python 3 compatibility to CWL Tool, Schema Salad and CWL Test...
Implement algorithms for the generation of high-resolution isotope patterns
Contributor: Nikos Patikas
In mass spectrometry the isotope pattern of an unknown molecule consists a powerful analytical tool to identify its molecular formula. Modern...
antiSMASH Migration to Template System
Contributor: Mariana Nave
antiSMASH, a python-based tool to mine micro-organisms genomes, currently uses pyQuery to generate static HTML pages. Consequently, several...
ETE/Tree matcher
Contributor: Dimitris Pliakos
TreeMatcher is a subproject of ETE3. Target of TreeMatcher is to perform search on phylogenetic trees using tree patterns that allows relax...
GeneNetwork Genome Browser
Contributor: Christian Fischer
Modify GeneNetwork to embed the BioDalliance genome browser in it. BioDalliance (henceforth BD) would be integrated into GeneNetwork (henceforth GN);...
Common Workflow Language reference implementation modernization- Making cwltool and schema-salad, Microsoft Windows compatible and providing complete Python 3 support for cwltool and schema-salad
Contributor: Kapil kumar
Cwltool is a reference implementation of the Common Workflow Language. It provides comprehensive validation of CWL files and include tools related to...
Bionode-Watermill - A Streaming Workflow Engine for Bioinformatics
Contributor: Tiago Jesus
This project started in last GSoC but is still missing core functionality
openSNP: Linking Phenotypes to SNPs in openSNP
Contributor: Vivek Rai
A crucial component of the openSNP infrastructure is to make the available data more accessible to the general users and scientists alike. Currently,...
Bionode workflow engine for streamed data analysis
Contributor: thejmazz
The streams based workflow engine will organize tasks into streams, allow parallelization of this streams, and work locally as well as integrated...
openSNP: Extending Quantified-Self Support in openSNP
Contributor: gdyer
Over 100,000 people have already been genotype through DTC genetic testing however, these data live in siloes, often inaccessible to the public....
Automated tool wrapper/converter for CWL
Contributor: Anton Khodak
The project is aimed to generate CWL tool descriptions from Python tools which use argparse.
OpenSNP
Contributor: mateusjabour
We all know that nowadays a website needs a responsive layout, by the fact that there are a lot of different devices sizes, like smartphones, tablets...
Improve the prediction for RiPP clusters
Contributor: MNave
Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a class of secondary metabolites that share a common biosynthetic...
GeneNetwork Genome Browser
Contributor: christian_f
Modify GeneNetwork to embed the BioDalliance genome browser in it. BioDalliance (henceforth BD) would be integrated into GeneNetwork (henceforth GN);...