Grid-based Coupled Electron and Electromagnetic field Dynamics (GCEED) is an open-source software package for massively parallel first-principles calculations of electron dynamics in real time and real space. The program codes are written in the Fortran 90/95 language with MPI and OpenMP. Time dependent density functional theory (TD-DFT) calculations can be performed on 100,000 CPU cores of K Computer with high parallel efficiency.
Grid-Enabled Molecular Simulation Repository (GEMS)
Accurately predicts disease association of single nucleotide mutations
GESPA (GEnomic Single nucleotide Polymorphism Analyzer) is a bioinformatics tool for classifying Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs). GESPA predicts if a nsSNP is pathogenic using reports from literature and various algorithms to assess conservation in orthologous and paralogous protein alignments. Using reports from literature, GESPA is also able to predict the phenotype of a nsSNP with high accuracy. The software can be used clinically to determine if observed nsSNPs are associated with disease. A host of annotations are provided: orthologous and paralogous multiple sequence alignments, UCSC annotations, reports detailing conservation of a nsSNP in alignments, and links to external nsSNP and gene information such as relevant publications. GESPA is connected to a constantly updating SQL server allowing for fast data retrieval. NOTE: REQUIRES Java 1.7.0+. Port 1433 cannot be blocked by firewall, network, or antivirus program. Please cite: http://tinyurl.com/oj7p84a
A library of optimized parameters and example source code for the use of generalized Langevin equation in molecular dynamics.
An effort to have a open source SRS (Sequence Retrieval System), alternative to lion bioscience's one
GOCART is a modular open-source application used to assemble biological sequences into Gene Ontology (GO) annotated contigs for Web GUI visualization based on their corresponding hierarchal GO structure, described by the Gene Ontology Consortium.
GPSR is a resource for genomics, proteomics and systems biology. The aim of this project is to build comprehensive resources in the field of bioinformatics.
GParticles is a tool to simulate the growth behaviour of two- and three-dimensional nano particles based on a simple grid model, with adjustable (time-dependent) concentrations of the particle's different components.
GSim - free software tool for visualisation and processing of experimental and simulated nuclear magnetic resonance (NMR) spectra.
Gabedit is a Graphical User Interface for FireFly (PC-Gamess), Gamess-US, Gaussian, Molcas, Molpro, MPQC, NWChem, OpenMopac, Orca, PSI4 and Q-Chem computational chemistry packages.
GamaComp - A graph comparative metabolic pathway tool to find shortest path using JUNG Library.
Gaussian Output Tools is a package of simple scripts to extract data from Gaussian output files.
Generation of molecular formulas by high-resolution MS and MS/MS data
This is an open source implementation of molecular formula calculation by high resolution MS and MS/MS data as described in M. Meringer, S. Reinker, J. Zhang, A. Muller: MS/MS Data Improves Automated Determination of Molecular Formulas by Mass Spectrometry. MATCH Commun. Math. Comput. Chem. 65, 259-290, 2011. The software user manual is available here: https://www.researchgate.net/publication/307964728_MOLGEN-MSMS_Software_User_Manual Example MS and MS/MS data files for GenForm can be downloaded here: https://sourceforge.net/p/genform/code/HEAD/tree/trunk/data/ A first program call could look like this: GenForm ms=SinapinicAcidMs.txt msms=SinapinicAcidMsMs.txt exist out
This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.
The Generic Genetic Studies Database (GGSD) is a web-based, relational database driven data management software package for the management of large scale genetic studies.
A visual editor for the definition of Carbohydrate structures, computation of masses and derivation of fragments.
Gromacs GUI is a graphical user interface for popular molecular dynamics package Gromacs. For more information see: http://resal.wordpress.com/gromacs-gui/
Calculate growth rates from microplate reader output
GrowthRates uses the output from microbial growth rate experiments that are done using microtiter plate readers to caculate the best-fit growth rates, the lag times and the maximum OD.
GVIB is a user friendly package for vibrational analysis. Given a molecular geometry, it will calculate vibrational frequencies and intensities using anharmonic internuclear potential.
HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.
Library written in C with Python API for IPv6 networking
This project is a rewritten of an initial project that I've called GLUE and created in 2005. I'm trying to readapt it for Python 2.7.3 and GCC 4.6.3 The library has to be build as a simple Python extension using >python setup.py install and allows to create different kind of servers, clients or hybryds (clients-servers) over (TCP/UDP) using the Ipv6 Protocol. The architecture of the code is based on neuron architecture. Will put an IPv6 adress active (one or more on my wireless network card) as soon as possible available so that you can download codes.
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.
A simple tool for molecular biologists (or similar) to estimate the size of electrophoresis gel bands. This can be applied to SDS-Page-,Native-Protein-, DNA, RNA, *whatever* gels as long as a weight/size standard lane is present on the gel.
General purpose de novo molecular design software
Although many potential applications exist in chemistry and material science, software to allow the general application of de novo structure-based design methods in supramolecular chemistry was non-existent. To address this limitation we created HostDesigner, a code that builds and evaluates millions of molecules in minutes. This command line executable builds 3D molecular structures by covalently connecting user-defined input fragments with pre-computed hydrocarbon fragments from a library. The results are ranked with respect to desired geometric constraints defined by the user. See the User's Manual for further details including a list of literature citations for example applications. Download includes User's Manual, HostDesigner 4.0 source code (in Fortran), data files, example input, HDViewer executables for MacOS, Linux, and Windows, and mengine source code (in C). HostDesigner was developed and posted by author Dr. Benjamin P Hay