Category: Miscellaneous

OFF-TARGET PIPELINE 1.5.4.2 -Identify Off-targets of Pharmaceuticals

OFF-TARGET PIPELINE 1.5.4.2

:: DESCRIPTION

OFF-TARGET PIPELINE is a platform intended to carry out a recently introduced chemical systems biology approach for secondary target identification, but may also be useful to other applications in bioinformatics and drug discovery. Researchers can predict and compare protein functional sites, conduct structure-based docking, compute binding energy and compare electrostatic potential distribution within cavities. It also supports normalization of docking scores, information retrieval from PDB, and parsing of output files. All the afore-mentioned procedures are parallelized with significant speed gains and labor savings.

::DEVELOPER

Thomas Evangelidis (tevang3@gmail.com)

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 OFF-TARGET PIPELINE

:: MORE INFORMATION

References:

L. Xie, J. Wang and P.E. Bourne 2007
“In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Esterogen Receptor Modulators“.
PLoS Comp. Biol., 3(11):e217

GeneLink 1.7 – Data Management System to Facilitate Genetic Studies of Complex Traits

GeneLink 1.7

:: DESCRIPTION

GeneLink is a data management system designed to facilitate genetic studies of complex traits.In contrast to gene-mapping studies of simple Mendelian disorders, genetic analyses of complex traits are far more challenging, and high quality data-management systems are often critical to the success of these projects. For this reason, we have developed GeneLink, a Web-accessible, password-protected Sybase database that enables genotypic data to be merged easily with pedigree and extensive phenotypic data. GeneLink was designed specifically to facilitate large-scale (multi-center), genetic linkage or association studies and is a powerful tool for complex trait mapping. GeneLink securely and efficiently handles large amounts of data, as well as provides additional features to facilitate quality control and analysis of data generated. In particular, chromosome-specific data files containing marker data in genetic map order can be downloaded in various formats appropriate for downstream analyses (e.g. GAS, LINKAGE). Furthermore, an unlimited number of phenotypes (either qualitative or quantitative) can be stored and analyzed. Finally, GeneLink generates several quality assurance reports, including genotyping success rates of specified DNA samples or success and heterozygosity rates for specified markers. GeneLink has already proven an invaluable tool for complex trait mapping studies and is discussed primarily in the context of our large, multi-center study of hereditary prostate cancer (HPC).

:DEVELOPER

NHGRI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Unix
  • Sybase SQL
  • Perl
  • Apache

:: DOWNLOAD

  GeneLink

:: MORE INFORMATION

Citation:

Gillanders, E.M., Masiello, A., Gildea, D., Umayam, L., Duggal, P., Klein, A., Jones, M., Freas-Lutz, D., Ibay, G., Trout, K., Wolfsberg, T.G., Trent, J.M., Bailey-Wilson, J.E., Baxevanis, A.D. 2004.
GeneLink: A Database to Facilitate Genetic Studies of Complex Traits.
BMC Genomics 5(1):81.

ANDY 0.2 – Large Biological Database Searching on Computer Clusters

ANDY 0.2

:: DESCRIPTION

ANDY  (seArch coordination aND analYsis)  is a set of Perl programs and modules for easily running large biological database searches, and similar applications, over the nodes of a Linux/Unix computer cluster in order to achieve speedup through parallelization. Users specify their cluster runs through a straightforward XML configuration file, in which they specify a template for the pipeline or sequence of commands they want to run on the nodes, as well as the locations and types of data sources for the command lines and other information.

::DEVELOPER

Computational Genomics Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Perl

:: DOWNLOAD

  ANDY

:: MORE INFORMATION

Citation:

Andrew Smith,John-Marc Chandonia,Steven E. Brenner
ANDY: a general, fault-tolerant tool for database searching on computer cluster
Bioinformatics (2006) 22 (5): 618-620

SeqHound 3.02 – Bioinformatics Database Warehouse Resource

SeqHound 3.02

:: DESCRIPTION

SeqHound is a freely available bioinformatics database warehouse resource that collects bioinformatics data from a number of sources including the National Center for Biotechnology Information and the Gene Ontology Consortium. It is designed for programmers who need unrestricted access to up-to-date data.

::DEVELOPER

Department of Biochemistry, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl
  • Java

:: DOWNLOAD

 SeqHound

:: MORE INFORMATION

Citation

Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW.
SeqHound: biological sequence and structure database as a platform for bioinformatics research.
BMC Bioinformatics. 2002 Oct 25;3:32. Epub 2002 Oct 25.

MassiveSAR – Small molecule structural similarity analysis and clustering

MassiveSAR

:: DESCRIPTION

MassiveSAR is a software for analysis of high-throughput screening data and generally for analysis of data sets containing multiple chemical compounds. This software is most suitable for finding related chemical structures and for establishing structure-activity relationships (SAR) within experimentally generated molecule sets or libraries of small molecules.

::DEVELOPER

BiochemLabSolutions.com

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 MassiveSAR

:: MORE INFORMATION

ELN 4.05 – Electronic Lab Notebook

ELN 4.05

:: DESCRIPTION

ELN (Electronic Lab Notebook) focuses on user convenience. Due to high degree of automation, it is easy to keep organized and well-maintained records with minimum efforts. Among the key strengths are the ability to prove that a record was made on a certain date, ability to share the data with any number of colleagues and ability to hyperlink pages within ELN. For example, if today’s result relates to an experiment from another day, month or year, it is possible to mutually link both pages. The entire ELN has a non-proprietary HTML format and can be viewed on any computer and any OS, even without installing this program.

::DEVELOPER

BiochemLabSolutions.com

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 ELN

 

:: MORE INFORMATION

As is, the software runs in a freeware mode. If you like the program, please obtain the license.

Mouse Atlas Data Analysis CD-ROMs 0403

Mouse Atlas Data Analysis CD-ROMs 0403

:: DESCRIPTION

Mouse Atlas data and software is available in a set of CD-ROMs.

Software CD contains software that can be installed on a users own computer.The software includes the MAPaint and Java WlzViewer programs. These programs allow the user to view the Mouse Atlas 3D models and anatomy domains in any plane. MAPaint can also be used to paint and define arbitrary regions in 2D and 3D space. A suite of utility programs is also included, that enables manipulation of spatial data, and conversion from the Mouse Atlas woolz image format to more common image formats (jpg, tif, etc.).

Data CD contain the set of MouseAtlas 3D models.The models can be used in conjunction with the software to browse the 3D structures, identify anatomy components, and prepare data for inclusion in the database of gene expression

::DEVELOPER

 EMAP • Human Genetics Unit • Medical Research Council

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac OsX

:: DOWNLOAD

  Mouse Atlas Data Analysis CD-ROMs 

:: MORE INFORMATION

BioStat 5.3.0 – Biology Statistical Software

BioStat 5.3.0

:: DESCRIPTION

BioStat is a user-friendly biology and medicine oriented statistical software.With BioStat 2009, one gets a robust suite of statistics tools and graphical analysis methods that are easily accessed though a simple and straightforward interface.

::DEVELOPER

AnalystSoft Inc

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 BioStat

:: MORE INFORMATION

Buy

DensityFit 1.0 – Analysis of Electronic Density Map for Protein

DensityFit 1.0

:: DESCRIPTION

DensityFit combines a low-resolution electronic density map for a protein (usually obtained by electron microscopy) and an atomic-resolution structure (usually obtained by X-ray crystallography) of the same protein in a different conformation in order to predict the atomic-resolution structure of the conformation described by the density map.

::DEVELOPER

Konrad Hinsen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 DensityFit

:: MORE INFORMATION

Citation:

K Hinsen, N Reuter, J Navaza, D L Stokes, and J J Lacapere
Normal mode based fitting of atomic structure into electron density maps:application to SR Ca-ATPase
Biophys. J. 88:818-827 (2005)

ARCADE 0.1 beta – Query and Visualize Data from Multiple Databases

ARCADE 0.1 beta

:: DESCRIPTION

ARCADE (A Real Time Comparative Analysis Display Environment) performs comparative queries over two or more distributed and potentially heterogeneous databases.The existence of large amounts of genomic information from many species on different databases means that sophisticated tools are required to retrieve the information important to a user and to display it a coherent manner. Furthermore, since information about one species can be used to aid research on closely related species there is great need for tools to be able to perform complex comparative queries. For example, the conserved gene order found in some cereals may be exploited to locate homologous genes in related species. ARCADE is a software tool for carrying out such comparative queries across many different sources and to display the results of these queries in a suitable coherent format.

::DEVELOPER

 DICKS COMPUTATIONAL BIOLOGY GROUP

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX
  • JAVA

:: DOWNLOAD

 ARCADE

:: MORE INFORMATION

Citation:

Couchman M, Davenport G and Dicks J (2002)
A real-time comparative analysis display environment (ARCADE).
Genome Informatics, Hinxton