Tag: Toolkit

WIST 1.1 – The Workflow Information Storage Toolkit

WIST 1.1

:: DESCRIPTION

WIST is a template-based toolkit to facilitate rapid LIMS (Laboratory Information Management System) development. WIST is designed to create LIMS modules with a web-based front end and a SQL database back end, along with a repository for larger data objects (e.g., files) that are impractical to store in SQL tables.

::DEVELOPER

The VIMSS (Virtual Institute of Microbial Stress and Survival)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX / Windows
  • Apach
  • MySQL
  • Perl

:: DOWNLOAD

 WIST

:: MORE INFORMATION

Citation

WIST: toolkit for rapid, customized LIMS development.
Huang YW, Arkin AP, Chandonia JM.
Bioinformatics. 2011 Feb 1;27(3):437-8. doi: 10.1093/bioinformatics/btq676. Epub 2011 Jan 21.

svmPRAT 1.0 – svm-Based Protein Residue Annotation Toolkit

svmPRAT 1.0

:: DESCRIPTION

svmPRAT is a general purpose protein residue annotation toolkit to allow biologists to formulate residue-wise prediction problems. svmPRAT formulates annotation problem as a classification or regression problem using support vector machines. The key features of svmPRAT are its ease of use to incorporate any user-provided information in the form of feature matrices. For every residue svmPRAT captures local information around the reside to create fixed length feature vectors. svmPRAT implements accurate and fast kernel functions, and also introduces a flexible window-based encoding scheme that allows better capture of signals for certain prediction problems.

::DEVELOPER

Huzefa Rangwala

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

  svmPRAT

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2009 Dec 22;10:439.
svmPRAT: SVM-based protein residue annotation toolkit.
Rangwala H, Kauffman C, Karypis G.

Mavric 0.8.3 – Python toolkit for Phylogenetics

Mavric 0.8.3

:: DESCRIPTION

Mavric is a python module for the manipulation and visualization of phylogenetic trees. It is also a recursive acronym for Mavric Visualizes Rick’s Cladograms :) It aims to be a user-friendly tool for manipulating phylogenetic trees on *NIX-like systems, especially Linux. As such it complements other phylogeny programs like those in the PHYLIP package, which for all their strengths currently lack a nice graphical interface.

::DEVELOPER

Rick Ree rree at oeb.harvard.edu.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python

:: DOWNLOAD

 Mavric

:: MORE INFORMATION

LoopTK 2.0.1 – Protein Loop Kinematic Toolkit

LoopTK 2.0.1

:: DESCRIPTION

LoopTK (Protein Loop Kinematic Toolkit)is a C++ based object-oriented toolkit which models the kinematics of a protein chain and provides methods to explore its motion space. In LoopTK, a protein chain is modeled as a robot manipulator with bonds acting as arms and the dihedral degree of freedoms acting as joints. LoopTK is designed specifically to model the kinematics of protein loops, but it can be used to analyze the motion of any part of the protein chain. LoopTK provides methods for sampling the conformation space of protein loops as well as the self motion space of a loop. Example applications for LoopTK include x-ray crystallography, homology modeling, and drug design.

::DEVELOPER

LoopTK Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 LoopTK

:: MORE INFORMATION

Citation

P. Yao, A. Dhanik, N. Marz, R. Propper, C. Kou, G. Liu, H. van den Bedem, J.C. Latombe, I. Halperin-Landsberg, R.B. Altman.
“Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops“,
IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 5, pp. 534-545, 2008. (2008)

SimTK Core 2.1 – Simbios Biosimulation ToolKit

SimTK Core 2.1

:: DESCRIPTION

SimTK Core is one of the two packages that together constitute SimTK, the biosimulation toolkit from the Simbios Center. The SimTK Core is a collection of libraries which provide basic numerical methods for simulating biological structures. The SimTK Core consists of 6 libraries: SimTKlapack (linear algebra), SimTKcommon (basic matrix and vector operations), SimTKcpodes (ordinary differential equations and differential algebraic equations), SimTKmath (optimization, and numerical differentiation), SimTKsimbody (multibody dynamics), and SimTKmolmodel (molecule modeler that builds Simbody models of molecules). There is also an optional li-brary SimTKsimbody_aux that can be used for visualizing Simbody simulations using VTK.

SimTK, the Simbios biosimulation toolkit, provides a robust, high-performing, open-source collection of technologies that are valuable for building applications that employ physics-based simulations of biological structures. It is well-suited for applications in a wide variety of domains from molecules to whole organisms.

::DEVELOPER

SimTK Core Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

  SimTK Core

:: MORE INFORMATION

Citation:

Jeanette P. Schmidt, Scott L. Delp, Michael A. Sherman, Charles A. Taylor,Vijay S. Pande, Russ B. Altman,
“The Simbios National Center: SystemsBiology in Motion“,
Proceedings of the IEEE, special issue on Computational System Biology. Volume 96, Issue 8:1266 – 1280. (2008)