Science and medicine

Open Bioinformatics Foundation (OBF)

Open Source & Open Science in biological research

cc++javascriptpythonfrontendreactcssgitgithubhtml

Organization website

Participation history

7 GSoC years

2022 2021 2020 2019 2018 2017 2016

2022

5 projects

Official year page

Feature Viewer - Enhanced User Experience and Performance

Analyzing positional features/annotations in sequences is important in bioinformatics. Visualizing such data is quite a challenging task, considering...

Code Project page

Migration of the backend to Express, GraphQL, and MongoDB

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...

Code Project page

Journal tracker – finalise and deploy React front-end

The project aims at helping researchers find journals that require open source code easily. I aim to create a user interface that could seamlessly...

Code Project page

Efficient data layout for mass spectrometry data (OpenMS)

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...

Code Project page

Genestorian data refinement

Genstorian data refinement tool is pipeline to identify allele names in genotype of a model organism and strain information related to the allele...

Code Project page

2021

8 projects

Official year page

Implementations of AVX-512 functions

This project aims to add portable implementations for SIMD ISA extension AVX-512 functions which are not yet supported by SIMDe. This will make...

Code Project page

Developing WellcomeML further for the visualisation of academic research data

Synopsis WellcomeML is a python package containing a set of utility functions that use machine learning for reading, processing, embedding and...

Code Project page

Enabling and prototyping JavaScript visualizations in the Qt-based viewer TOPPView (OpenMS).

This project aims to enable JavaScript visualizations in TOPPView using Qt WebEngine and its different modules.

Code Project page

Implementation of NEON functions (SIMDe)

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...

Code Project page

Design and implementation of Code is Science front-end using ReactJS

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...

Code Project page

Data streaming in scientific workflows, implementation for Toil

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...

Code Project page

gtfBase- A curated resource of multispecies genomic regions

While GTF files are by themselves comprehensive, a lot of analysis is focused on individual features. For example, any analysis focused on...

Code Project page

Development of a user interface to visualise VEP data using neXtProt tools

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...

Code Project page

2020

8 projects

Official year page

Implementation of SVML in SIMDe

This project will be aimed to create an API-compatible open-source implementation of Intel's proprietary SVML which would be portable to other...

Code Project page

OpenMS R-Package

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...

Code Project page

Parallel Graph Traversal for Variation Graphs

Traditionally, Bioinformatics has focused its eﬀorts on the study of single genomes, each representing an individual of a certain species. In more...

Code Project page

Implementing user-friendly search features

Pysradb provides a convenient method to retrieve information from NCBI’s SRA database. Currently, pysradb is transitioning to phase out its...

Code Project page

Healthcare-Researcher-Connector (HRC): A Federated Learning package for bridging the gap between Healthcare providers and researchers

Nowadays, sharing and use of human biomedical data is heavily restricted and regulated by multiple laws. Such data-sharing restrictions allow keeping...

Code Project page

SIMDe : Add implementations of ISA extensions (SSE4.2 and AVX512) and NEON implementations of SSE4.1,SSE4.2,SSE3,SSSE3 ISA extension

The project deals with writing portable implementations for SIMD ISA extensions SSE4.2 and AVX-512 functions and NEON implementations for...

Code Project page

Protein sequence and structural analysis CWL pipeline for comparative biology

While there are a multitude of open source ML methods for prediction of various structural or biological related attributes, there are no open source...

Code Project page

Using DeNovo Sequencing to Predict Protein Database Suitability

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...

Code Project page

2019

5 projects

Official year page

antiSmash submission redesign

antiSmash run multiple instances of the submission page, depending on whether people want to analyse bacterial or fungal sequences, or run the...

Code Project page

Add Variant Graph (VG) support to BioD

The current representation of reference genomes is as a sequence of nucleotides akin to a long string. Intuitively, this doesn’t represent a genome...

Code Project page

BAM to ADAM converter on Sambamba’s base

This project is aimed to build an efficient BAM format to ADAM format converter utilizing Sambamba library base.

Code Project page

Interactive Yeoman generator for BioJS components

BioJS is a library of over one hundred JavaScript components enabling users to visualise and process data using current web technologies. BioJS makes...

Code Project page

Add blockchain and hyperledger support for the ‘Journal of Open Data Publications’

Open science is a movement that promotes open access to research data, publications, and scientific collaboration. It promises to increase...

Code Project page

2018

5 projects

Official year page

Adding methods to cobrapy for improved constraint-based metabolic modelling.

Constraint-Based Reconstruction and Analysis (COBRA) methods for Genome-wide Metabolic Networks (GEMs) have proven to be essential for the varied...

Code Project page

Frontend Website Student Project for BioJS

BioJS is a library of over two hundred JavaScript components which enables users to visualise and process data. BioJS currently has two websites: ...

Code Project page

Implement the support for Research Object specification into Nextflow framework

The goal of this project is to implement the support for Research Object specification into Nextflow workflow framework, with the aim to improve the...

Code Project page

Improve Posterior Error Probability Estimation For Peptide Search Engine Results

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...

Code Project page

Backend Website Student Project

BioJS is a library of over two hundred JavaScript components enabling developers to visualize and process data using current web technologies. The...

Code Project page

2017

7 projects

Official year page

Adding Python 3 compatibility and improving mypy support for cwltool

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...

Code Project page

Implement algorithms for the generation of high-resolution isotope patterns

In mass spectrometry the isotope pattern of an unknown molecule consists a powerful analytical tool to identify its molecular formula. Modern...

Code Project page

antiSMASH Migration to Template System

antiSMASH, a python-based tool to mine micro-organisms genomes, currently uses pyQuery to generate static HTML pages. Consequently, several...

Code Project page

ETE/Tree matcher

TreeMatcher is a subproject of ETE3. Target of TreeMatcher is to perform search on phylogenetic trees using tree patterns that allows relax...

Code Project page

GeneNetwork Genome Browser

Modify GeneNetwork to embed the BioDalliance genome browser in it. BioDalliance (henceforth BD) would be integrated into GeneNetwork (henceforth GN);...

Code Project page

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

Cwltool is a reference implementation of the Common Workflow Language. It provides comprehensive validation of CWL files and include tools related to...

Code Project page

Bionode-Watermill - A Streaming Workflow Engine for Bioinformatics

This project started in last GSoC but is still missing core functionality

Code Project page

2016

7 projects

Official year page

openSNP: Linking Phenotypes to SNPs in openSNP

A crucial component of the openSNP infrastructure is to make the available data more accessible to the general users and scientists alike. Currently,...

Code Project page

Bionode workflow engine for streamed data analysis

The streams based workflow engine will organize tasks into streams, allow parallelization of this streams, and work locally as well as integrated...

Code Project page

openSNP: Extending Quantified-Self Support in openSNP

Over 100,000 people have already been genotype through DTC genetic testing however, these data live in siloes, often inaccessible to the public....

Code Project page

Automated tool wrapper/converter for CWL

The project is aimed to generate CWL tool descriptions from Python tools which use argparse.

Code Project page

OpenSNP

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...

Code Project page

Improve the prediction for RiPP clusters

Ribosomally synthesised and post-translationally modified peptides (RiPPs) are a class of secondary metabolites that share a common biosynthetic...

Code Project page

GeneNetwork Genome Browser

Modify GeneNetwork to embed the BioDalliance genome browser in it. BioDalliance (henceforth BD) would be integrated into GeneNetwork (henceforth GN);...

Code Project page