Python Bio-Informatics Software

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Browse free open source Python Bio-Informatics Software and projects below. Use the toggles on the left to filter open source Python Bio-Informatics Software by OS, license, language, programming language, and project status.

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  • 1

    miRge3

    Comprehensive analysis of small RNA sequencing data

    An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User Interface (GUI). For more details refer to documentation link below.
    Downloads: 13 This Week
    Last Update:
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  • 2
    Febrl (Freely Extensible Biomedical Record Linkage) does data standardisation (segmentation and cleaning) and probabilistic record linkage ("fuzzy" matching) of one or more files or data sources which do not share a unique record key or identifier.
    Downloads: 2 This Week
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  • 3
    Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.
    Downloads: 5 This Week
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  • 4
    A univariate and multivariate analysis UI. This project is no longer under development. Please use as you wish.
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    Downloads: 3 This Week
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  • 5
    This project is A Mitochondrial OxydoReduction Simulation System. It consists of two linked projects: a program for displaying and analysing large biomolecular systems (Floral) and a multi-agent simulator for biomolecular oxydoreduction systems (AMORSS).
    Downloads: 2 This Week
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  • 6
    ABE is a small, fast and convenient program for visualizing and modeling experimental bioassay data. The data can be modeled using either polynomials or a more specific four-parameter model based upon the standard, sigmoidal dose-response curve.
    Downloads: 0 This Week
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  • 7
    Affymetrix GeneChip Operating Software (GCOS) is used to control Affymetrix Microarray scanners and fluidic stations. Using the DCOM API, this project provides programmatic scripting of GCOS using Python.
    Downloads: 0 This Week
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  • 8

    Atlas2Cloud

    Atlas2 Genome Analysis Pipeline on Amazon Web Services

    This is the backend source code of the Atlas2-Cloud pipeline on Amazon which starts and terminates worker nodes, runs analysis and monitors worker instances. It is PRIMARILY meant to be used through Amazon Web Services (AWS) management console by looking for the public Atlas2-Cloud machine image. Alternatively, the code can also be used for running the pipeline from your computer. By installing this software on your computer you will be setting up your computer to act as the head node which would then run the pipeline from your computer.
    Downloads: 0 This Week
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  • 9
    Volumetric file viewer for the human brain. Easy, powerful and flexible fMRI/MRI brain research and clinical neuro-surgery tool. Using state of the art open VTK 3D library, the proven Qt GUI toolkit, coded in Python.
    Downloads: 0 This Week
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  • 10
    Copy Number Analysis for Targeted Resequencing (CONTRA) is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.
    Downloads: 0 This Week
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  • 11
    A web-based system for upoading, managing, sharing, and analyzing bioinformatic data. The system is primarily written in python, and runs on both linux and MacOs.
    Downloads: 0 This Week
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  • 12

    Clinical Evidence Detector

    Detector of clinical evidence

    This is a Python program based on the NegEx algorithm that detects the polarity of the clinical evidence in clinical random trials. If you use this code please cite this paper: P. Davis-Desmond and Diego Mollá. Detection of Evidence in Clinical Research Papers (2012). Australasian Workshop On Health Informatics and Knowledge Management (HIKM 2012), Melbourne, Australia. http://www.ics.mq.edu.au/~diego/publications/hikm12.pdf
    Downloads: 0 This Week
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  • 13
    Laboratory notebook using version control system and independent date-time stamping (as notarization), in order to ensure record accountability, auditing, and conforming to US FDA 21 CFR 21's rule on electronic records. Please kindly rate this application or drop me an email at [ mauriceling AT acm DOT org ] so that I can hear from you. Otherwise, I have no idea who the users are. Please kindly help.
    Downloads: 0 This Week
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  • 14
    DEODAS designs & analyzes consensus-degenerate oligonucleotide probes for biological research. DEODAS automatically designs and screens, probes against databases of known genes & stores the information in a searchable database.
    Downloads: 0 This Week
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  • 15
    DNAID software is a tool for assessing confidence in biological identifications made by comparing DNA sequences. It allows DNA sequences to be placed within a taxonomy and determines confidence in matches of a query sequence to each taxon.
    Downloads: 0 This Week
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  • 16
    DrPangloss is a python implementation of a three operator genetic algorithm, complete with a java swing GUI for running the GA and visualising performance, generation by generation
    Downloads: 0 This Week
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  • 17
    A Python library bringing together utilities I've written over the years for work in bioinformatics and biostatistics, which should be generally applicable outside these fields as well. Focuses on string processing, DBI, and math.
    Downloads: 0 This Week
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  • 18

    Erda

    Workflow automation of Thomas networks

    This script is supplementary to the article "Time series dependent analysis of unparametrized Thomas networks" and performs the workflow steps described in section 7.
    Downloads: 0 This Week
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  • 19
    A database and a web front end for physiologic data on animal feeding, developed with PostgreSQL and Django at NESCent (http://www.nescent.org) for Mammalian Feeding Working Group (http://www.feedexp.org). Current development of the codebase is on Github at http://github.com/NESCent/feedingdb.
    Downloads: 0 This Week
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  • 20

    FingerID

    Metabolite identification via machine learning.

    [NOTICE!] FingerID since version 1.4 will be hosted on github: https://github.com/icdishb/fingerid A metabolite identification software using tandem mass spectrometry and kernel methods. The related paper can be found at http://bioinformatics.oxfordjournals.org/content/early/2012/07/18/bioinformatics.bts437.abstract. Now it supports unix/linux like system.
    Downloads: 0 This Week
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  • 21

    GCB_package

    Stand-alone version of the Genome Complexity Browser

    This application allows observing genome rearrangements in prokaryotic genomes. It provides rearrangements frequencies profiles and genomes graph representation.
    Downloads: 0 This Week
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  • 22
    Genetic programming environment to inference context free grammars base on positive and negative examples of language.
    Downloads: 0 This Week
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  • 23
    GUI for DEDA

    GUI for DEDA

    GUI for DEmography Data Analysis

    <This project has been completely rewrote and transformed into a new one: https://sourceforge.net/projects/deday/. 2013/06/26> The graphic user interface for DEDA (DEmography Data Analysis), a scientific software package fitting survivalship data to a number of distributions using maximum likelihood (ML) method. Currently, Weibull (2p), Gompertz and Gompertz-Makeham are supported. IMPORTANT NOTICE: Only the GUI is provided here. In order to perform the analysis, one also need the DEDA computation core program. Please email a request to me, entitled: 'Request for DEDA computation core', if you wish to have a copy.
    Downloads: 0 This Week
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  • 24

    Genetic data converter

    Convert genetic data for hapmixmap software

    Genetic data converter, for hapmap.org and hapmixmap data formats. Reads data in tabular format and writes in hapmixmap format. It's possible to add extensions to output different data formats.
    Downloads: 0 This Week
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  • 25
    A small simulator for Mendelian genetics, genetic drift, natural selection and random mutations, built on matplotlib and wxpython. A graph will be generated that traces the distribution of genotypes at successive generations.
    Downloads: 0 This Week
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