The Wayback Machine - https://web.archive.org/web/20200918173202/https://github.com/topics/computational-biology

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computational-biology

Here are 487 public repositories matching this topic...

3dmol / 3Dmol.js

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WebGL accelerated JavaScript molecular graphics library

computational-biology molecular-graphics computational-chemistry molecular-modeling

Updated Sep 11, 2020
Jupyter Notebook

opensim-org / opensim-core

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SimTK OpenSim C++ libraries and command-line applications, and Java/Python wrapping.

science engineering simulation biological-simulations computational-biology biomechanics computational-science

Updated Sep 18, 2020
C++

rasbt / biopandas

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Working with molecular structures in pandas DataFrames

bioinformatics pdb molecular-structures pandas-dataframe protein-structure molecule computational-biology drug-discovery molecules mol2 pdb-files

Updated Aug 4, 2020
Python

Mariewelt / OpenChem

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OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

machine-learning deep-neural-networks deep-learning computational-biology pytorch computational-chemistry drug-discovery drug-design predictive-modeling graph-convolutional-networks qsar

Updated Jul 24, 2020
Python

opencobra / cobrapy

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Open

cobra.test.create_test_model("salmonella") results in incorrect exchange reaction names

5

jeremymchacon commented Aug 25, 2020

Hello maintainers of the amazing package,

I recently updated cobrapy and am experienced unexpected behavior with cobra.test.create_test_model("salmonella")

Two things are unusual:

Now, many warnings are given during loading of the model, whereas none were given in a previous version. Here are a few of the warnings:

`Model does not contain SBML fbc package information.
SBML package

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SBML good first issue help-wanted

Open

Fix test cases that use deprecated behaviour

Open

fix: avoid scrambling of group members

9

Find more good first issues →

dash-cytoscape

plotly / dash-cytoscape

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Open

[Feature Request] expand/collapse of nodes

2

aloktiagi commented Aug 3, 2020

Hi,

It would be nice to have the capability to expand/collapse nodes similar to https://github.com/iVis-at-Bilkent/cytoscape.js-expand-collapse.

Thanks.

Read more

good first issue suggestion

Open

Dash Cytoscape: control the scroll wheel sensitivity for zooming

3

Open

Improve interactions tests

seq-lang / seq

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A high-performance, Pythonic language for bioinformatics

python programming-language bioinformatics compiler genomics computational-biology domain-specific-language

Updated Sep 9, 2020
C++

asoplata / open-computational-neuroscience-resources

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A publicly-editable collection of open computational neuroscience resources

awesome computational-biology neuroscience computational-neuroscience open-science awesome-list neuroimaging-data neuroscience-methods neuroscience-data neural-simulators electrophysiological-data

Updated Sep 11, 2020

Benjamin-Lee / deep-rules

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Ten Quick Tips for Deep Learning in Biology

data-science machine-learning bioinformatics deep-learning genomics biology computational-biology manuscript manubot

Updated Sep 17, 2020
HTML

eselkin / awesome-computational-neuroscience

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Open

Add departments for Stanford

eselkin commented Jul 27, 2019

Add departments column and values for PIs at Stanford University

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good first issue

Open

Add department for Caltech

Open

Add departments to University of Waterloo

bioSyntax / bioSyntax

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Syntax highlighting for computational biology

syntax-highlighting vim less bioinformatics pdb sublime-text computational-biology gedit vcf fasta bam

Updated Feb 10, 2020
Shell

aquaskyline / Clairvoyante

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Clairvoyante: a multi-task convolutional deep neural network for variant calling in Single Molecule Sequencing

bioinformatics deep-learning computational-biology variant-calling

Updated Feb 13, 2020
Python

msmbuilder / vde

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Variational Autoencoder for Dimensionality Reduction of Time-Series

python deep-learning time-series molecular-dynamics computational-biology pytorch computational-chemistry variational-autoencoder

Updated Jul 29, 2019
Jupyter Notebook

aquaskyline / SOAPdenovo2

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Next generation sequencing reads de novo assembler.

bioinformatics genome assembly computational-biology soapdenovo

Updated Jul 23, 2019
C

markovmodel / deeptime

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Deep learning meets molecular dynamics.

python markov-model machine-learning deep-learning time-series tensorflow computational-biology pytorch computational-chemistry autoencoder data-analysis dimension-reduction

Updated May 3, 2019
Jupyter Notebook

pnpnpn / dna2vec

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dna2vec: Consistent vector representations of variable-length k-mers

python nlp machine-learning bioinformatics neural-network word2vec word-embeddings ml computational-biology embeddings

Updated Aug 27, 2020
Python

sorgerlab / indra

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INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

nlp bioinformatics biology modeling systems-biology computational-biology pysb indra sbml

Updated Sep 18, 2020
Python

jisungk / RIDDLE

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Race and ethnicity Imputation from Disease history with Deep LEarning

machine-learning bioinformatics deep-learning biology computational-biology neural-networks imputation epidemiology

Updated Jul 17, 2018
Python

a-r-j / graphein

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Protein Graph Library

bioinformatics deep-learning structural-biology protein-data-bank protein-structure computational-biology pytorch protein protein-design geometric-deep-learning graph-neural-networks dgl

Updated Sep 16, 2020
Jupyter Notebook

biotite

biotite-dev / biotite

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A comprehensive library for computational molecular biology

bioinformatics structural-biology computational-biology sequence-analysis

Updated Sep 17, 2020
Python

fbrundu / pymrmr

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Python3 binding to mRMR Feature Selection algorithm (currently not maintained)

data-science computational-biology feature-selection

Updated Sep 14, 2020
C++

HKU-BAL / Clair

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Clair: Exploring the limit of using deep neural network on pileup data for germline variant calling

bioinformatics deep-learning computational-biology variant-calling

Updated Sep 4, 2020
Python

Bohdan-Khomtchouk / shinyheatmap

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Web application for enormous biological heatmaps

r web-server heatmap computational-biology high-performance-computing graphics-rendering interactive-biological-heatmaps

Updated Jul 18, 2020
R

Chaste / Chaste

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Chaste - Cancer Heart And Soft Tissue Environment - main public repository

c-plus-plus computational-biology electrophysiology mathematical-modelling hpc-applications cancer-research mathematical-biology developmental-biology cell-based physiology

Updated Sep 11, 2020
C++

burkesquires / python_biologist

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Python Programming for Biologists

python programming-language bioinformatics programming biology computational-biology python3 biology-education

Updated Aug 12, 2020
Python

BALL-Project / ball

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The Biochemical Algorithms Library

c-plus-plus structural-biology computational-biology force-field chemoinformatics drug-design

Updated May 25, 2020
C++

chanzuckerberg / idseq-web

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Infectious Disease Sequencing Platform

science bioinformatics research genomics biology sequencing computational-biology next-generation-sequencing bioinformatics-pipeline global-health virology infectious-diseases metagenomic idseq idseq-web

Updated Sep 18, 2020
JavaScript

montilab / hypeR

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An R Package for Geneset Enrichment Workflows

bioinformatics computational-biology geneset-enrichment-analysis

Updated Sep 16, 2020
R

Bohdan-Khomtchouk / Biochat

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Natural language processing of Gene Expression Omnibus data

nlp metadata natural-language-processing bioinformatics lisp common-lisp computational-biology integrative-analysis metadata-extraction gene-expression-omnibus

Updated May 1, 2019
Common Lisp

universal-automata / liblevenshtein-java

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Various utilities regarding Levenshtein transducers. (Java)

computer-science search-engine data-science machine-learning natural-language-processing information-retrieval bioinformatics genomics dictionary fuzzy-search computational-biology edit-distance levenshtein-distance approximate-string-matching distance-metric finite-state-automata finite-state-transducer levenshtein-automata spelling-correction universal-automata

Updated Apr 6, 2018
Java

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