Showing 47 open source projects for "computational biology"

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  • 1
    CGAL

    CGAL

    The Computational Geometry Algorithms Library

    CGAL or the Computational Geometry Algorithms Library is a C++ library that gives you easy access to a myriad of efficient and reliable geometric algorithms. These algorithms are useful in a wide range of applications, including computer aided design, robotics, molecular biology, medical imaging, geographic information systems and more. CGAL features a great range of data structures and algorithms, including Voronoi diagrams, cell complexes and polyhedra, triangulations, arrangements of curves...
    Downloads: 10 This Week
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    DeepChem

    DeepChem

    Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, etc

    ... an individual pip Installation. The DeepChem project maintains an extensive collection of tutorials. All tutorials are designed to be run on Google collab (or locally if you prefer). Tutorials are arranged in a suggested learning sequence that will take you from beginner to proficient at molecular machine learning and computational biology more broadly.
    Downloads: 0 This Week
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  • 3
    Systems Biology Markup Language (SBML)

    Systems Biology Markup Language (SBML)

    A file format for exchanging computational models in systems biology

    The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.
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    Downloads: 75 This Week
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  • 4
    SBW (Systems Biology Workbench)

    SBW (Systems Biology Workbench)

    Framework for Systems Biology

    The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as SED-ML...
    Downloads: 10 This Week
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  • 5
    CyberUnits

    CyberUnits

    Class library for computational cybernetics

    CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal.
    Downloads: 2 This Week
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  • 6

    Palibino

    Pascal library for bioinformatics

    Palibino is a class library for Object Pascal supporting bioinformatics, large-scale genomic analysis in life sciences and computational biology.
    Downloads: 0 This Week
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  • 7

    AngClust

    AngClust: Angle-based feature clustering for time series

    Citation: Aimin Li, Siqi Xiong, Junhuai Li, Saurav Mallik, Yajun Liu, Rong Fei, Hongfang Zhou, Guangming Liu. AngClust: Angle Feature-Based Clustering for Short Time Series Gene Expression Profiles. January 2022. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM. DOI: 10.1109/TCBB.2022.3192306 Full text: https://ieeexplore.ieee.org/document/9833353/ https://pubmed.ncbi.nlm.nih.gov/35853049/ Highlights * We proposed a novel clustering algorithm based...
    Downloads: 0 This Week
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  • 8
    CSBB-v2.1 [CSBB-v3.0 is now available]

    CSBB-v2.1 [CSBB-v3.0 is now available]

    Computational Suite For Bioinformaticians and Biologists

    CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX...
    Downloads: 0 This Week
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  • 9
    CSBB-v3.0

    CSBB-v3.0

    CSBB - Computational Suite for Bioinformaticians and Biologists

    CSBB is a command line-based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java, python and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX...
    Downloads: 0 This Week
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  • 10
    Nuvarator

    Nuvarator

    A SNV Detection Software Tools Installer Package

    A software package Nuvarator which downloads and installs different tools related to Somatic SNV detection. SNV detection is range of computational tech- niques and algorithms used to identify the existence of single nu- cleotide variants (SNVs) by using the result from Next Generation Sequencing (NGS) experiments. NGS are methods employed for Whole Genome Sequencing, a process for determining the precise order of nucleotides within a DNA molecule which can improve the knowledge available...
    Downloads: 0 This Week
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  • 11
    isiKnock

    isiKnock

    In silico knockouts for signaling pathways

    ... and Amstein et al. 2017. Hannig et al. (2019) isiKnock: in silico knockouts in signaling pathways, Bioinformatics, 35(5), 892–894 Amstein et al. (2017) Manatee invariants reveal functional pathways in signaling networks. BMC systems biology, 11(1), 72. Scheidel et al. (2016) In silico knockout studies of xenophagic capturing of Salmonella. PLoS computational biology, 12(12), e1005200.
    Downloads: 1 This Week
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  • 12
    KMC-KaiC

    KMC-KaiC

    Kinetic Monte Carlo simulation of the in-vitro Kai Circadian clock

    ... clock", which is freely available at the open access journal PLOS Computational Biology: https://doi.org/10.1371/journal.pcbi.1005415 *UPDATE* We made a fully reversible version of our model, including the inverse reactions for ATP hydrolysis. This makes it possible to run the model at thermodynamic equilibrium. This version of the model can be downloaded under KMC_KaiC_Rev.zip. If you like to use our model for your own research, please cite our PLoS Computational Biology paper.
    Downloads: 0 This Week
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  • 13
    CSBB-v2.0

    CSBB-v2.0

    Computational Suite for Bioinformaticians and Biologists

    CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R, java and ruby in background for specific modules. Major focus of CSBB is to allow users from biology and bioinformatics community, to get benefited by performing down-stream analysis tasks while eliminating the need to write programming code. CSBB is currently available on Linux, UNIX...
    Downloads: 0 This Week
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  • 14
    Ben(Zai)Ten is a graphical modeling environment for computational and systems biology. It supports the community exchange standards: SBML, SBRML, SED-ML as well as ontologies: MIRIAM, SBO, ChEBI, KEGG, GO
    Downloads: 0 This Week
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  • 15
    SUPERmerge

    SUPERmerge

    ChIP-seq coverage island analysis algorithm for broad histone marks

    SUPERmerge is a ChIP-seq read pileup analysis and annotation algorithm for investigating alignment (BAM) files of diffuse histone modification ChIP-seq datasets with broad chromatin domains at a single base pair resolution level. SUPERmerge allows flexible regulation of a variety of read pileup parameters, thereby revealing how read islands aggregate into areas of coverage across the genome and what annotation features they map to within individual biological replicates. SUPERmerge is...
    Downloads: 0 This Week
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  • 16

    MultiCellDS

    MultiCellular Data Standards Project

    MultiCellDS (Multicellular data specification), an outgrowth of the earlier MultiCellXML project, aims to create a data standard for sharing multicellular experimental, simulation, and clinical data. Our ultimate goal is to foster a community that develops user-friendly tools that can read, write, and recombine data into better simulations and analyses for multicellular biology and predictive medicine. As part of this effort, we are developing MultiCellDB: a repository for a curated libary...
    Downloads: 0 This Week
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  • 17

    Opera

    An optimal genome scaffolding program

    ...-rich eukaryotic genomes with performance guarantees. Genome Biology, May 2016, doi: 10.1186/s13059-016-0951-y. Song Gao, Wing-Kin Sung, Niranjan Nagarajan. Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of Computational Biology, Sept. 2011, doi:10.1089/cmb.2011.0170.
    Downloads: 6 This Week
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  • 18
    HeatmapGenerator
    ... suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline." Source Code for Biology and Medicine, 2014 9:30] HeatmapGenerator source code is available at: https://github.com/Bohdan-Khomtchouk/HeatmapGenerator Bohdan Khomtchouk wishes to acknowledge the support of the Department of Defense (DoD) through the National Defense Science & Engineering Graduate Fellowship (NDSEG) Program. HeatmapGenerator is released under the GNU GPL.
    Downloads: 13 This Week
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  • 19

    evoNet

    Deep learning for population genetic inference

    This software implements the algorithms described in the following paper: Sheehan, S. and Song, Y.S. Deep learning for population genetic inference. PLoS Computational Biology, in press.
    Downloads: 0 This Week
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  • 20

    yTOS

    Metabolic pathways to Systems Biology standards (SBGN and SBML)

    yTOS enables transformation of metabolic pathways generated in yEd graph editor into a computational model defined by Systems Biology standards: SBGN (Systems Biology Graphical Notation) format and SBML (Systems Biology Markup Language) with CellDesigner annotations. yTOS takes as input a graphML file. The example of Glycolysis given with yTOS tool was adopted from http://www.sbgn.org/Documents/PD_L1_Examples . Requirements: Java 1.8 is necessary.
    Downloads: 0 This Week
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  • 21

    DEAPathways

    Differential Expression Analysis for Pathways

    This project contains the source code associated with the PLoS Computational Biology publication: "Differential Expression Analysis for Pathways". The paper text can be found here: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002967
    Downloads: 0 This Week
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  • 22

    DESN

    Differential activE sub-Network (DEN): R/Bioconductor based package

    ... in discerning differential gene expression across diverse conditions. Computational biology is in need of methods for integration of static networks and gene expression data, since it provides interesting insights into the dynamics of biological systems. DEN is an R/Bioconductor based package designed to assemble different types of human bio-molecular interactions as a complete interactome and contains functions to extract dynamic active networks by integration of gene expression data.
    Downloads: 0 This Week
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  • 23

    Automatic cell lineage reconstruction

    Automatic segmentation and tracking for 3D time-lapse microscopy

    From Amat et al., Nature Methods, 2014*: "The comprehensive reconstruction of cell lineages in complex multicellular organisms is a central goal of developmental biology. We present an open-source computational framework for segmentation and tracking of cell nuclei with high accuracy and speed. We demonstrate its (1) generality, by reconstructing cell lineages in four-dimensional, terabyte-sized image data of fruit-fly, zebrafish and mouse embryos, acquired with three different types...
    Downloads: 0 This Week
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  • 24

    LipidWrapper

    Create lipid-bilayer models of arbitrary geometry.

    ..., is capable of creating curved membrane models with geometries derived from various possible sources, both experimental and theoretical. We are hopeful that this utility will be a useful tool for the computational-biology community.
    Downloads: 0 This Week
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  • 25

    Top-down Modulated Pitch Model

    An implementation for the Top-Down pitch model by E.Balaguer et al.

    MATLAB implementation for the Top-Down Modulated Pitch model proposed by Balaguer-Ballester E., Clark, N., Coath, M., Krumholz, K. and Denham, S. L. in "Understanding Pitch Perception as a Hierarchical Process with Top-Down Modulation", published in "PLOS Computational Biology" in 2009
    Downloads: 0 This Week
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