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A molecular weight calculator written in Visual Basic.
A molecular weight calculator written in Visual Basic. Unfortunately, it is only for 64-bit Windows at this time.
The code files (.sln) are downloadable only. I can't figure out Git.
Least-squares fit of amylopectin chain-length distribution
...The amylopectin CLD biosynthesis model used by this program is explained in the article “A Parameterized Model of Amylopectin Synthesis provides key insights into the Synthesis of Granular Starch”, by Alex Chi Wu, Matthew K. Morell and Robert G. Gilbert.
The downloadable .zip file contain the main code readily usable after compiling. An instruction manual is also provided.
This is an open source program.
Smoldyn is a computer program for simulating reactions and diffusion at a mesoscopic size scale. This scale lies between the more traditional microscopic size scale, in which all or most atoms are considered.
The Protein Geometry Database hosts the development code for a flexible database for searching protein geometry, as well as a library for accessing this data for protein modeling & refinement programs.
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MOLGENIS can be used to generate databases for life science experiments (micrroarray, mass spectrometry, genomics) having a web user interface, csv exchange format, and programmatic interfaces (web services, rest, and r-project). See NatRevGen 8.
SynBioLib -- your toolkit for synthetic biology applications. SynBioLib aims to establish a platform on which the Synthetic Biology community can develop and share code that is common to many tasks and programs.
The Blue Obelisk is a group of scientists driven by a belief in Open Source, Open Standards and Open Data, expressed in code, data, algorithms, specifications, tutorials, demonstrations, articles and anything that helps get the message across.
Datagam is a tool for extracting data from output or punch files produced by GAMESS(US) or FireFly (old name PC GAMESS) packages. Mac GUI wrapper also available.
Upstream version of the project goes to the launchpad. Only final versions of the sourcecode and compiled binars will be available from this domain.
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.
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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 sourcecode repository can be found on https://jchempaint.github.io
Molevolve is a Java library for running a Genetic Algorithm to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations. Requires JDK 1.5.