Open Source Mac Bio-Informatics Software
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Bio-Informatics Software for Mac
View 15 business solutionsBrowse free open source Bio-Informatics software and projects for Mac below. Use the toggles on the left to filter open source Bio-Informatics software by OS, license, language, programming language, and project status.
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PyRx - Virtual Screening Tool
Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. PyRx also includes chemical spreadsheet-like functionality and powerful visualization engine that are essential for Rational Drug Design. Please visits PyRx home page to learn more about PyRx and watch videos on how to use it. -
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Gwyddion
Scanning probe microscopy data visualisation and analysis
A data visualization and processing tool for scanning probe microscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry data, useful also for general image and 2D data analysis. -
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Jmol
An interactive viewer for three-dimensional chemical structures.
Over 1,000,000 page views per month. Jmol/JSmol is a molecular viewer for 3D chemical structures that runs in four independent modes: an HTML5-only web application utilizing jQuery, a Java applet, a stand-alone Java program (Jmol.jar), and a "headless" server-side component (JmolData.jar). Jmol can read many file types, including PDB, CIF, SDF, MOL, PyMOL PSE files, and Spartan files, as well as output from Gaussian, GAMESS, MOPAC, VASP, CRYSTAL, CASTEP, QuantumEspresso, VMD, and many other quantum chemistry programs. Files can be transferred directly from several databases, including RCSB, EDS, NCI, PubChem, and MaterialsProject. Multiple files can be loaded and compared. A rich scripting language and a well-developed web API allow easy customization of the user interface. Features include interactive animation and linear morphing. Jmol interfaces well with JSpecView for spectroscopy, JSME for 2D->3D conversion, POV-Ray for images, and CAD programs for 3D printing (VRML export). -
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Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
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smina
Scoring and Minimization with AutoDock Vina
A fork of AutoDock Vina that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project. -
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Toxtree: Toxic Hazard Estimation
Toxicity prediction for chemical compounds
A GUI application which estimates toxic hazard of chemical compounds. The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation and Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Skin sensitisation reactivity domain -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction -Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC) -Structural Alerts for Functional Group Identification (ISSFUNC) -Structural alerts associated with covalent protein binding and DNA binding. - Ames mutagenicity Toxtree provides a plugin framework to incorporate different approaches to the estimation. Platform independent (written in Java), with the use of The Chemistry Development Kit. -
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nmrshiftdb2 is a NMR database (web database) for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. The nmrshiftdb2 software is open source, the data is published under an open content license. The core of nmrshitdb2 are fully assigned spectra with raw data and peak lists (we have pure peak lists as well). Those datasets are peer reviewed by a board of reviewers. The project is supported by a scientific advisory board. nmrshiftdb2 is part of the NFDI4Chem initiative (https://nfdi4chem.de/) and will provide a component for a curated repository there. Please consult the documentation for more detailed information.
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Design PCR primers from DNA sequence. Widely used (190k Google hits for "primer3"). From mispriming libraries to sequence quality data to the generation of internal oligos, primer3 does it. C&perl. Developers/testers/documenters needed.
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Free DELTA
Software tools for processing taxonomic descriptions in DELTA format
The Free DELTA Project is a free, open-source, software alternative for a generic system to the processing of taxonomic descriptions based on the DELTA (DEscription Language for TAxonomy) format. -
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PerlPrimer is a GUI application written in Perl that designs primers for standard PCR, bisulphite PCR and Real-time PCR (QPCR). It aims to automate and simplify the process of primer design.
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The MolTools Java library provides tools for building applications that handle nucleotide sequence data. Features include sequence I/O, handling of lists/databases of sequences, calculation of Tm, and other utilities for sequence design.
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AlphaGenome
Programmatic access to the AlphaGenome model
The AlphaGenome API provides access to AlphaGenome, Google DeepMind’s unifying model for deciphering the regulatory code within DNA sequences. This repository contains client-side code, examples, and documentation to help you use the AlphaGenome API. AlphaGenome offers multimodal predictions, encompassing diverse functional outputs such as gene expression, splicing patterns, chromatin features, and contact maps. The model analyzes DNA sequences of up to 1 million base pairs in length and can deliver predictions at single-base-pair resolution for most outputs. AlphaGenome achieves state-of-the-art performance across a range of genomic prediction benchmarks, including numerous diverse variant effect prediction tasks. -
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kallisto
Near-optimal RNA-Seq quantification
kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a transcriptome index, that in itself can take more than 10 minutes to build. And since it uses pseudoalignment, it is robust to errors in the reads and preserves the key information needed for quantification. This makes kallisto not only fast but highly accurate as well. In many benchmarks, it even greatly outperforms existing tools. -
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A set of tools for working with VCF files, such as those generated by the 1000 Genomes Project. This project is migrating to github: https://vcftools.github.io/
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VarScan
Variant detection in next-generation sequencing data
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes. THE LATEST VERSION IS AVAILABLE ON GITHUB -
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picard
A set of tools for working with high-throughput sequencing data
A set of tools (in Java) for working with next generation sequencing data in the SAM/BAM format. Note that development has moved to GitHub at https://github.com/broadinstitute/picard and support is available on the GATK forum at http://gatkforums.broadinstitute.org/categories/ask-the-team -
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Combenefit
Synergy analyses of drug and other other agent combinations
Combenefit software is a standalone application for Windows that performs surface analyses of drug and other agent combinations to identify synergy. Please cite as: "Di Veroli,G.Y. et al. (2016) Combenefit: an interactive platform for the analysis and visualization of drug combinations. Bioinformatics." (http://bioinformatics.oxfordjournals.org/content/early/2016/05/27/bioinformatics.btw230.abstract) Current version (2.021): https://sourceforge.net/projects/combenefit/files/Combenefit%202.02%20WIN_64%20%28PREFERRED%29/ Older version for 32-bit os: https://sourceforge.net/projects/combenefit/files/WIN_32/ Quick user's guide: https://sourceforge.net/projects/combenefit/files/Combenefit_v2.02_quick_guide_v1.03.pdf/download Examples: https://sourceforge.net/projects/combenefit/files/Examples/ Template file: https://sourceforge.net/projects/combenefit/files/REPLICATE_TEMPLATE.xls/download -
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BioXTAS RAW
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF as well as electron density reconstructions using DENSS. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) or the regularized alternating least squares (REGALS) methods. Active source code is now maintained on github: https://github.com/jbhopkins/bioxtasraw To install: Check the instructions available at: http://bioxtas-raw.readthedocs.io/en/latest/install.html and in the Files tab. User guides: RAW guides are available at: http://bioxtas-raw.readthedocs.io/ and in the Files tab. To contact us, see: https://bioxtas-raw.readthedocs.io/en/latest/help.html -
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CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage. It was written in ANSI compliant C. See the README file for more information.
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A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
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GelJ
GelJ is a Java program for the analysis of DNA gel fingerprints images
GelJ is a Java application designed for analysing DNA fingerprint images. GelJ is a feather-weight, user-friendly, open-source and free tool that combines the simple design of free systems with instrumental features for DNA fingerprinting that are only available on commercial tools. Some of the outstanding features of GelJ are functionality for accurate lane- and band-detection, several methods for computing migration models and generating dendrograms, comparison of banding patterns from different experiments, and database support. Citing GelJ: J. Heras, C. Domínguez, E. Mata, and V. Pascual. GelJ – a tool for analyzing DNA fingerprint gel images. BMC Bioinformatics 2015, 16:270 http://doi.org/10.1186/s12859-015-0703-0. You can see more information about GelJ in https://sourceforge.net/p/gelj/wiki/Home/ Several videos explaining the use of GelJ are available in https://sourceforge.net/p/gelj/wiki/Videos/ Please address any question or comment to joheras at gmail.com -
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Open Drug Discovery Toolkit (ODDT)
Modular and comprehensive toolkit for use in cheminformatics
Open Drug Discovery Toolkit (ODDT) is modular and comprehensive toolkit for use in cheminformatics, molecular modeling etc. ODDT is written in Python, and makes extensive use of Numpy/Scipy. You can use any supported toolkit united under common API (for reference see Pybel or Cinfony). All methods and software based on Pybel/Cinfony should be drop-in compatible with ODDT toolkits. In contrast to its predecessors, which were aimed to have minimalistic API, ODDT introduces extended methods and additional handles. These extensions allow to use of toolkits at all its grace and some features may be backported from others to introduce missing functionalities. Most important and handy property of Molecule in ODDT are Numpy dictionaries containing most properties of supplied molecule. Some of them are straightforward, other require some calculation, ie. atom features. Dictionaries are provided for major entities of molecules. -
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HaploView is a Java based tool for use by biologists in the study of genetic haplotype data. It provides a quick, easy interface to many common tasks involved in such analyses. Please go to the homepage below for the latest version!
