Biology Experiments

This project hosts the 'Simulation Tool', an extensible, interactive environment for carrying out simulation experiments of SBML models. This project can use RoadRunner or SBW enabled simulators to carry out simulations.

Set of python scripts that can be used for the calculations of equilibrium fractionation factors from experiments and from statistical mechanics theory. python scripts use Scipy/Numpy/Matplotlib/WxPython for calculations, plotting and the GUI

Jam is an easy-to-use self-contained data acquisition and analysis system for VME-based (or CAMAC-based) nuclear physics experiments. Jam has an easy, standard GUI for taking and sorting multi-parameter event-based data into 1-d and 2-d histograms.


Platforms: Windows, Mac, Solaris, Linux

LabDiary is a program for managing laboratory experiments in a sophisticated way. It is very easy to use - you can link experiments logically with each other, associate files to an experiment and structure all your data.


Platforms: Windows, Mac, Linux

A python package that allows scientists to easily create configurable and reusable experiments. Intended for use with the LabRAD framework. Developed by the Haeffner group studying quantum simulation at UC Berkeley. Wiki at lrexp.wikispaces.com


Platforms: Windows, Mac, Linux

ELGE - Environment for language games experiments.


Platforms: Windows, Mac, Linux

This project houses software to analyze data acquired from electrophysiology experiments. Currently, we have an Octave/MATLAB program to analyze electroneurogram traces of coupled oscillators, and a Perl library for the analysis of voltage trace data


Platforms: Windows, Mac, Linux

Maple Tree is a Java based visualization tool used by researchers in the biological sciences to visualize and graphically browse the results of analyses of gene expression data collected from microarray experiments.


Platforms: Windows, Mac, Linux

Metmask is a tool written in python for managing chemical identifiers for metabolomics experiments. It can incorporate identifiers from local textfiles, several online databases, query PubChem and record all found associations in a local sqlite database.


Platforms: Windows, Mac, Linux

This software is to help the those connected with Biology,Biotechnology,Bio Informatics.The user can select from the choices of proteins, nucleotides,etc(All those found on NCBI's website)and search for the specific results


Platforms: Windows, Mac, BSD, Linux

The class libraries here provide infrastructure for creating simulations of low energy nuclear physics experiments, as well as some useful working programs that do simple simulations and analysis of experiments performed with magnetic spectrographs.


Platforms: Windows, Mac, Linux

Open2Dprot is an open-source proteomics project for the development of bioinformatic tools for n-dimensional protein expression data analysis of quantified protein expression across multiple samples from research experiments.


Platforms: Windows, Mac, Linux

PyExPsiN is a Python crossplatform (Linux/Windows) module for made easy writing psychological experiments. Right now includes functions for DMTS (Delayed Matching to Sample), N-Back, Spatial N-Back, 'Grammatical', Mixed Dots, Stroop, and more.


Platforms: Windows, Mac, Linux

PEACH provides C++ functions for programming experiments in visual psychophysics. PEACH contains an extensive collection of visual primitives as well as a set of experimental functions, which allow to code a complicated experiment in a few dozen lines.


Platforms: Mac, Linux

'Plasmidb' is a database management system (RDMS) used to manipulate, view and store molecular biology information rapidly and easily. Editable information includes: constructed plasmids, clones, standard vectors, primers, antibiotics, enzymes and more


Platforms: Windows, Mac, Linux

an experimentation page for art made with Processing


Platforms: Windows, Mac, Linux

RADlab needs your donations!! Features: * Radiation Detection Experiments * Gamma, beta, alpha and neutron sources * Coincidence Experiment * NIM module and instrumentation * Easy setup


Platforms: Mac

The Systems Biology Results Markup Language is a language describing data. Unlike flat data formats, SBRML allows describing the origin of the data as well. This project hosts a library and tools for using SBRML.


Platforms: Windows, Mac, Linux

Create, check, annotate, merge, diff, split SBML (System Biology Markup Lanugage) documents. The latest version of semanticSBML is webbased with a RESTful interface.


Platforms: Windows, Mac, Linux

Java class libraries for structural biology development: includes protein format conversion tool, printf-based text formatting, Pred2ary secondary structure prediction, neural net library, Hooke-Jeeves global optimizer, and misc. math & statistics.


Platforms: Windows, Mac, Linux