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AutoPrime allows to rapidly design primers for real-time PCR measurement of eukaryotic expression.
By connecting to the EnsEMBL database gene structure information is used to find primers spanning exon borders. This way only expressed sequences are captured. Additionally mispriming on repetitive regions can be avoided using information from RepBase.
Chemical Evaluation Framework (CEF) is a molecular structure based software to assist in hazard assessment. Download requires Java 6 update 1. Sourcecode is contained in jar files. Download contains GSH reactivity plugin.
CIPTCL is a set of applications for the management of the Tissue Culture Lab at the International Potato Center. It supports handling, tracking and location of clonal plant materials including data logging on hand-held PCs with wireless and bar-code.
dictyBase is a database application for Dictyostelium genomics. The database software is intended to be of general use and usage of our software by other similar projects is encouraged. Thanks to the Saccharomyces Genome Database (SGD) for lots of code.
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Manuelito is a Java tool for decrypting posttranslational modification (PTM) patterns of proteins based on MALDI mass spectrometry spectra. It was built for analysing the 'histone code' but it can be applied to any other highly modified protein.
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.
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A toolbox for quantitative morphometric analysis of early development in spherical embryos, such as Xenopus laevis (African Clawed Frog). The toolbox is developed for Matlab 6.5 and higher and combines C-Mex code with Matlab functions.
Sight provides a friendly interface to create and connect agents for bioinformatics. The workflow supports multiple responses to a single request, structure transforms, filters and request history access.Can talk with ordinary http servers (get and post)
Set of Java packages to apply Genetic Algorithms to any kind of problem. Various genetic operators are implemented and an example shows of how the system could be applied to digital circuit evolution.
Mister Model is a code generation system. It takes a UML model expressed as XMI
and generates sourcecode specifically designed to work in a cross-platform web service environment. It fixes the legendary 'Serialization Failed' messages in web services
Pymerase is a tool intended to generate a python object model, relational database, and an object-relational model connecting the two. However it has been extended to also output webpages and can be easily extended to output whatever else you might like.
openevo is a project started to find out about behaviour of evolutionary generated machine code. It implements a certain set of CPU instruction codes and a few interrupts for interaction with the runtime environment.
Sequence studio main package provides classes and interfaces for various kinds of sequence alignment. Differently from regular expressions it computes similarity with two initially unknown strings. Project page provides code generating applet.
Jaybird is java-language based, source & xml & codebyte class inter-converting tool.
You can write your Envolvable Code with it;
You can make your computer write program itself;
You can run program without compiling time;
You can manage source as data
The Molecular Modeling Templates, MMT is a C++ class library for molecular simulation applications. MMT serves as a code basis that can be easily extended and modified to perform Monte Carlo and molecular dynamics simulations.
Virtual machine/emulator; "holding pen" for self-replicating programs written in custom RISC assembly-like language, evolving via random point mutations and periodic fitness-based cullings. Inspired (like Avida) by Thomas Ray's alife simulator, Tierra
Distributed Genetic Programming SRVM
(Simple Risc Virtual Machine)
Distributed function approximator of nonlinear functions with automatic induction of machine code.
A software framework to support distributed evolutionary software development. It dynamically creates a network of nodes that can run a pre-distributed sourcecode (e.g. artificial lifeforms). The results of the calculation will be sent back to the maste
Code repository for the Laboratory for Genome Bioinformatics at Texas A&M. The LGB project was initiated primarily to support biologists at Texas A&M needing help with bioinformatics in order to use new genomic technologies.