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         Molecular Science
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162 projects in result set. Projects sorted by: Ranking (Top Ranked First)
Select a page:   1   2   3   4   5   6   7   8   9   Next


1. ABFF - Project for develop force fields with using ab-initio calculations


  • Topic: Molecular Science, Chemistry
  • Programming Language: C++
  • Operating System: All 32-bit MS Windows (95/98/NT/2000/XP), 64-bit MS Windows, OS Portable (Source code to work with many OS platforms)
  • License: Academic Free License (AFL)
  • Intended Audience: Science/Research
  • Development Status: 2 - Pre-Alpha

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2. Agent-Based Multiscale Tissue Model - Agent-based multiscale model of cancer proliferation dynamics


  • Topic: Intelligent Agents, Simulations, Bio-Informatics, Molecular Science
  • Programming Language: Java
  • Operating System: OS Independent (Written in an interpreted language)
  • License: Academic Free License (AFL)
  • Intended Audience: Science/Research
  • Development Status: 3 - Alpha

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3. aisconvert - Toolkit for processing genetic data in RAW (23andme) format. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED conversion; regions of homozygousity


  • Topic: Bio-Informatics, Molecular Science
  • User Interface: Java Swing, Command-line
  • Programming Language: Java
  • Operating System: OS Independent (Written in an interpreted language), OS Portable (Source code to work with many OS platforms)
  • License: GNU General Public License (GPL)
  • Intended Audience: Advanced End Users
  • Development Status: 4 - Beta, 5 - Production/Stable

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4. AMORSS: redox enzymes simulation system - 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).

Click here to download.  
  • Topic: Molecular Science, Chemistry, Bio-Informatics, Simulations
  • User Interface: OpenGL, Command-line, wxWidgets, Tk
  • Programming Language: Python
  • Operating System: OS Independent (Written in an interpreted language), All POSIX (Linux/BSD/UNIX-like OSes)
  • License: GNU General Public License (GPL)
  • Intended Audience: Science/Research
  • Development Status: 3 - Alpha

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5. APBS - APBS is a software package for the numerical solution of the Poisson-Boltzmann equation, a popular continuum model for describing electrostatic interactions between molecular solutes over a wide range of length scales. <http://apbs.sf.net/>.

Click here to download.  
  • Topic: Chemistry, Physics, Mathematics, Molecular Science, Bio-Informatics, Simulations
  • User Interface: Command-line, Other toolkit
  • Translations: English
  • Programming Language: C, Fortran, Python
  • Operating System: Cygwin (MS Windows), 32-bit MS Windows (NT/2000/XP), All BSD Platforms (FreeBSD/NetBSD/OpenBSD/Apple Mac OS X), All POSIX (Linux/BSD/UNIX-like OSes), Linux, OS X, WinXP, SGI IRIX
  • License: MIT License, BSD License
  • Intended Audience: Science/Research, Education
  • Development Status: 5 - Production/Stable

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6. arrayplex - ArrayPlex integrates various forms of microarray data from diverse annotation and primary data sources. It provides a programmatic framework (API set) for collaborative development and deploys as easy to maintain client-server architecture.

Click here to download.  
  • Topic: Bio-Informatics, Molecular Science
  • User Interface: Java Swing
  • Translations: English
  • Programming Language: Java
  • Operating System: All BSD Platforms (FreeBSD/NetBSD/OpenBSD/Apple Mac OS X), All POSIX (Linux/BSD/UNIX-like OSes), All 32-bit MS Windows (95/98/NT/2000/XP)
  • License: GNU General Public License (GPL)
  • Intended Audience: Science/Research
  • Development Status: 4 - Beta
  • Database Environment: JDBC, PostgreSQL (pgsql)

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7. Ascalaph Graphics - Molecular Dynamics and Molecular Graphics program. Molecular model builder. Interface with the MDynaMix http://www.mmk.su.se/~sasha/mdynamix/


  • Topic: Research, Chemistry, Molecular Science
  • User Interface: OpenGL, Qt
  • Translations: English
  • Programming Language: C++, Fortran
  • Operating System: OS Portable (Source code to work with many OS platforms), Linux, WinXP, Windows 7
  • License: GNU General Public License (GPL)
  • Intended Audience: Advanced End Users, Developers, Education, Science/Research, Non-Profit Organizations
  • Development Status: 5 - Production/Stable

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8. Ascalaph Quantum - is a graphic interface and models builder for the quantum mechanics packages NWChem, CP2K and PC GAMESS/Firefly.


  • Topic: Quantum Computing, Molecular Science, Physics
  • User Interface: Qt, OpenGL
  • Programming Language: C++, Fortran
  • Operating System: OS Portable (Source code to work with many OS platforms), Linux, WinXP, Windows 7
  • License: GNU General Public License (GPL)
  • Intended Audience: Advanced End Users, Developers, End Users/Desktop
  • Development Status: 5 - Production/Stable

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9. Atomic-Clusters - This project is intended to perform Monte-Carlo-Simulations to calculate small clusters (2 to 13 atoms) of the rare gas "argon".

Click here to download.  
  • Topic: Molecular Science
  • User Interface: Console/Terminal
  • Translations: German
  • Programming Language: C
  • Operating System: OS Portable (Source code to work with many OS platforms)
  • License: GNU General Public License (GPL)
  • Intended Audience: Science/Research
  • Development Status: 4 - Beta

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10. AutoDock Software in Parallel with GPUs - Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/

Click here to download.  
  • Topic: Molecular Science, Medical Science Apps., Chemistry, Bio-Informatics
  • User Interface: Console/Terminal, Command-line
  • Translations: English
  • Programming Language: C, C++
  • Operating System: All BSD Platforms (FreeBSD/NetBSD/OpenBSD/Apple Mac OS X), All POSIX (Linux/BSD/UNIX-like OSes)
  • License: GNU General Public License (GPL)
  • Intended Audience: Science/Research, Healthcare Industry, Education, End Users/Desktop, Advanced End Users, Developers
  • Development Status: 4 - Beta

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11. Avogadro - Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.

Click here to download.  
  • Topic: Molecular Science, Chemistry, Visualization
  • User Interface: OpenGL, Qt
  • Translations: English, German, French, Italian, Spanish, Chinese (Simplified), Catalan, Chinese (Traditional), Russian, Brazilian Portuguese
  • Programming Language: C++, Python
  • Operating System: OS X, Linux, 32-bit MS Windows (NT/2000/XP), All POSIX (Linux/BSD/UNIX-like OSes), OS Portable (Source code to work with many OS platforms), WinXP
  • License: GNU General Public License (GPL)
  • Intended Audience: Science/Research, End Users/Desktop, Education, Advanced End Users
  • Development Status: 5 - Production/Stable

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12. BASILISK - BASILISK is a model of side chain conformational space in proteins. Unlike rotamer libraries, does BASILISK model the chi angles in continuous space. Furthermore features BASILISK an also continuous backbone dependence.


  • Topic: Molecular Science
  • User Interface: Console/Terminal
  • Programming Language: Python
  • Operating System: Linux, OS X
  • License: GNU General Public License version 3.0 (GPLv3)
  • Intended Audience: Advanced End Users, Developers, End Users/Desktop, Science/Research, Education
  • Development Status: 4 - Beta

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13. Bio-SPICE - Our goal is to create an open source framework and toolset for modeling dynamic cellular network functions, and to develop a user community committed to using, extending and exploiting these tools to further our knowledge of biologic processes.

Click here to download.  
  • Topic: Bio-Informatics, Simulations, Molecular Science, Medical Science Apps., Visualization
  • Translations: English
  • Operating System: OS Portable (Source code to work with many OS platforms)
  • License: BSD License
  • Intended Audience: Science/Research
  • Development Status: 4 - Beta

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14. Bioclipse - An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP).

Click here to download.  
  • Topic: Bio-Informatics, Chemistry, Visualization, Frameworks, Algorithms, Molecular Science
  • User Interface: Java SWT, Eclipse
  • Translations: English
  • Programming Language: Java
  • Operating System: OS Independent (Written in an interpreted language)
  • License: Eclipse Public License
  • Intended Audience: Science/Research, Healthcare Industry, End Users/Desktop
  • Development Status: 4 - Beta, 5 - Production/Stable
  • Database Environment: JDBC

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15. Bioinformatics Template Library - The original Bioinformatics Template Library (BTL) uses templates to implement generic programming in same way as the Standard Template Library (STL). Biolib aims at continue developing this library.


  • Topic: Molecular Science, Bio-Informatics
  • Programming Language: C++
  • Operating System: OS Portable (Source code to work with many OS platforms)
  • License: GNU General Public License (GPL)
  • Development Status: 4 - Beta

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16. Biological Network Analyzer - Workbench for visualizing biological networks (regulatory, interaction, and metabolic). Can be used as a front-end for BN++ databases, but also as stand-alone tool.

Click here to download.  
  • Topic: Molecular Science, Information Analysis, Visualization, Chemistry, Bio-Informatics
  • User Interface: Plugins, Java Swing
  • Translations: English
  • Programming Language: Java
  • Operating System: OS Independent (Written in an interpreted language)
  • License: GNU Library or Lesser General Public License (LGPL), GNU Library or "Lesser" General Public License version 3.0 (LGPLv3)
  • Intended Audience: Science/Research
  • Development Status: 3 - Alpha
  • Database Environment: MySQL, SQL-based

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17. Biomolecule Toolkit - The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools.

Click here to download.  
  • Topic: Molecular Science, Bio-Informatics, Frameworks
  • User Interface: Console/Terminal
  • Programming Language: C++
  • Operating System: OS Portable (Source code to work with many OS platforms), Linux, OS X
  • License: GNU Library or Lesser General Public License (LGPL)
  • Intended Audience: Developers, Science/Research
  • Development Status: 3 - Alpha

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18. BioNLP UIMA Component Repository - The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

Click here to download.  
  • Topic: Artificial Intelligence, Frameworks, Molecular Science, Information Analysis, Bio-Informatics
  • User Interface: Other toolkit
  • Programming Language: Java
  • Operating System: OS Independent (Written in an interpreted language)
  • License: GNU General Public License (GPL)
  • Intended Audience: Advanced End Users, Science/Research, Healthcare Industry, Developers
  • Development Status: 5 - Production/Stable, 4 - Beta

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19. BioSpring - BioSpring is a molecular simulation software based on spring network model, including non-bonded interactions, especially designed for Interactive Molecular Dynamics.


  • Topic: Molecular Science, Bio-Informatics, Simulations
  • Translations: French
  • Programming Language: C++
  • Operating System: Linux, OS X
  • License: GNU General Public License (GPL)
  • Intended Audience: Science/Research
  • Development Status: 3 - Alpha

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20. Bowtie - 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.

Click here to download.  
  • Topic: Search, Text Processing, Information Analysis, Molecular Science, Bio-Informatics
  • Programming Language: C++
  • Operating System: OS X, Linux, WinXP
  • License: Artistic License
  • Intended Audience: Science/Research
  • Development Status: 5 - Production/Stable

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162 projects in result set. Projects sorted by: Ranking (Top Ranked First)
Select a page:   1   2   3   4   5   6   7   8   9   Next

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