Open Source Java Molecular Science Software

Java Molecular Science Software

View 2692 business solutions

Browse free open source Java Molecular Science Software and projects below. Use the toggles on the left to filter open source Java Molecular Science Software by OS, license, language, programming language, and project status.

  • Our Free Plans just got better! | Auth0 Icon
    Our Free Plans just got better! | Auth0

    With up to 25k MAUs and unlimited Okta connections, our Free Plan lets you focus on what you do best—building great apps.

    You asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your security. Auth0 now, thank yourself later.
    Try free now
  • No-Nonsense Code-to-Cloud Security for Devs | Aikido Icon
    No-Nonsense Code-to-Cloud Security for Devs | Aikido

    Connect your GitHub, GitLab, Bitbucket, or Azure DevOps account to start scanning your repos for free.

    Aikido provides a unified security platform for developers, combining 12 powerful scans like SAST, DAST, and CSPM. AI-driven AutoFix and AutoTriage streamline vulnerability management, while runtime protection blocks attacks.
    Start for Free
  • 1
    Toxtree: Toxic Hazard Estimation

    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.
    Leader badge
    Downloads: 156 This Week
    Last Update:
    See Project
  • 2

    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
    Downloads: 15 This Week
    Last Update:
    See Project
  • 3
    SketchEl
    Chemical structure sketching tool, for use with various cheminformatics applications. Convenient to use and moderately sophisticated. Suitable for viewing, creating and editing MDL MOL files.
    Downloads: 10 This Week
    Last Update:
    See Project
  • 4
    The Sashimi project hosts the Trans-Proteomic Pipeline (TPP), a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to the open mzML/mzXML formats.
    Leader badge
    Downloads: 32 This Week
    Last Update:
    See Project
  • MongoDB Atlas | Run databases anywhere Icon
    MongoDB Atlas | Run databases anywhere

    Ensure the availability of your data with coverage across AWS, Azure, and GCP on MongoDB Atlas—the multi-cloud database for every enterprise.

    MongoDB Atlas allows you to build and run modern applications across 125+ cloud regions, spanning AWS, Azure, and Google Cloud. Its multi-cloud clusters enable seamless data distribution and automated failover between cloud providers, ensuring high availability and flexibility without added complexity.
    Learn More
  • 5
    RDKit

    RDKit

    Open-Source Cheminformatics and Machine Learning

    A collection of cheminformatics and machine-learning software written in C++ and Python. NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.
    Downloads: 11 This Week
    Last Update:
    See Project
  • 6
    MELTING is a software to compute, for a nucleic acid duplex, the enthalpy and the entropy of the helix coil transition and then the melting temperature. Four types of hybridization are possible : DNA/DNA, RNA/RNA, RNA/DNA and mRNA/RNA.
    Leader badge
    Downloads: 13 This Week
    Last Update:
    See Project
  • 7
    An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).
    Downloads: 7 This Week
    Last Update:
    See Project
  • 8
    MZmine 2

    MZmine 2

    A framework for differential analysis of mass spectrometry data

    MZmine 2 is a framework written in Java for differential analysis of mass spectrometry data.
    Leader badge
    Downloads: 14 This Week
    Last Update:
    See Project
  • 9
    Downloads: 7 This Week
    Last Update:
    See Project
  • Picsart Enterprise Background Removal API for Stunning eCommerce Visuals Icon
    Picsart Enterprise Background Removal API for Stunning eCommerce Visuals

    Instantly remove the background from your images in just one click.

    With our Remove Background API tool, you can access the transformative capabilities of automation , which will allow you to turn any photo asset into compelling product imagery. With elevated visuals quality on your digital platforms, you can captivate your audience, and therefore achieve higher engagement and sales.
    Learn More
  • 10
    JChemPaint Applet and Swing Application
    The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on https://jchempaint.github.io
    Downloads: 3 This Week
    Last Update:
    See Project
  • 11
    Ocean Optics Sample Pack

    Ocean Optics Sample Pack

    Sample code for Ocean Optics OmniDriver spectrometer device driver

    Sample code demonstrating how to use OmniDriver to drive Ocean Optics full range of spectrometers from C, C++, C#, Java, LabVIEW, Delphi, MATLAB and more.
    Downloads: 5 This Week
    Last Update:
    See Project
  • 12
    This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.
    Downloads: 5 This Week
    Last Update:
    See Project
  • 13
    NMRShiftDB
    NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data.
    Downloads: 4 This Week
    Last Update:
    See Project
  • 14
    mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
    Downloads: 4 This Week
    Last Update:
    See Project
  • 15
    NanoTrackJ

    NanoTrackJ

    NanoTrackJ - Size characterization of freely diffusing nanoparticles

    NanoTrackJ moved to GitHub! Please see: https://github.com/thorstenwagner/ij-nanotrackj or http://fiji.sc/NanoTrackJ
    Downloads: 2 This Week
    Last Update:
    See Project
  • 16
    J-ICE
    J-ICE stands for Jmol interface for crystallographic and electronic properties. Is an extension of the powerful, platform independent molecular visualizer Jmol, towards crystallographic and electronic properties. More info will be given soon.
    Leader badge
    Downloads: 3 This Week
    Last Update:
    See Project
  • 17
    JRC QSAR Model Database

    JRC QSAR Model Database

    (Q)SAR Model Reporting Format Inventory

    In the regulatory assessment of chemicals (e.g. under REACH), Quantitative Structure Activity Models (QSAR) are playing an increasingly important role in predicting properties for hazard and risk assessment. This implies both a need to be able to identify relevant QSARs and to use them to derive estimates and/or have access to their precalculated estimates. To help meet these needs, the JRC QSAR Model Database is established and freely accessible through http://qsardb.jrc.ec.europa.eu/qmrf The QSAR Model Reporting Format (QMRF) is a harmonised template for summarising and reporting key information on QSAR models, including the results of any validation studies. The information is structured according to the OECD validation principles. Download the QMRF Editor in order to describe your models in QMRF format and send the descriptions to JRC-COMPUTOX@ec.europa.eu to have them included in the database. More at http://qmrf.sourceforge.net/
    Downloads: 3 This Week
    Last Update:
    See Project
  • 18
    A collection of applets used to demonstrate physics and math principles. The applets include: a ray diagram drawing applet, a collision of disks applet, an electromagnetic field mapper and a 3d hydrogen orbital simulation.
    Downloads: 1 This Week
    Last Update:
    See Project
  • 19
    Janocchio is an application or applet for viewing 3D molecular structures and calculating NMR couplings and NOEs
    Downloads: 2 This Week
    Last Update:
    See Project
  • 20
    Octet is an object-oriented molecular representation framework written in Java.
    Downloads: 2 This Week
    Last Update:
    See Project
  • 21
    ProteinShader is a molecular visualization tool that can produce illustrative renderings of proteins that approximate what an artist might create using pen and ink. This free platform-independent program is written in Java and OpenGL Shading Language.
    Downloads: 1 This Week
    Last Update:
    See Project
  • 22
    4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
    Downloads: 1 This Week
    Last Update:
    See Project
  • 23
    Biological Network Analyzer
    Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BNDB datawarehouses, but also as stand-alone tool.
    Downloads: 1 This Week
    Last Update:
    See Project
  • 24
    The Hanalyzer is a tool designed to help biologists explain results observed in genome-scale experiments and to generate new hypotheses. It combines information extraction, semantic data integration, reasoning, and visualization.
    Downloads: 1 This Week
    Last Update:
    See Project
  • 25
    Modern MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Support available in Google group (https://groups.google.com/d/forum/13cmfa-openflux).
    Downloads: 1 This Week
    Last Update:
    See Project
  • Previous
  • You're on page 1
  • 2
  • 3
  • 4
  • 5
  • Next
Want the latest updates on software, tech news, and AI?
Get latest updates about software, tech news, and AI from SourceForge directly in your inbox once a month.