Tag: Computation

CentiLib – Computation of network centralities

CentiLib

:: DESCRIPTION

CentiLib is an Add-on for the computation and investigation of weighted and unweighted centralities in biological networks. Even though CentiLib was developed to integrate the computation of centralities into as many tools for the visualisation and analysis of biological networks as possible, it can be used for other types of networks, too.

::DEVELOPER

CentiLib team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 CentiLib 

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Apr 15;28(8):1178-9. Epub 2012 Mar 5.
CentiLib: comprehensive analysis and exploration of network centralities.
Gräßler J, Koschützki D, Schreiber F.

ABCRF 1.8 – Approximate Bayesian Computation via Random Forests

ABCRF 1.8

:: DESCRIPTION

ABCRF is an R library to perform Approximate Bayesian Computation (ABC) model choice and parameter inference via random forests.

::DEVELOPER

The Computational Biology Institute (IBC)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux /macOsX
  • R

:: DOWNLOAD

ABCRF

:: MORE INFORMATION

Citation

Bioinformatics. 2019 May 15;35(10):1720-1728. doi: 10.1093/bioinformatics/bty867.
ABC random forests for Bayesian parameter inference.
Raynal L, Marin JM, Pudlo P, Ribatet M, Robert CP, Estoup A

ABAG – Computation of Antibody/Antigen Concentration and Endpoint Titer

ABAG

:: DESCRIPTION

ABAG allows to compute the endpoint titer and concentration of Antibody(Ab) or Antigen(Ag) from ELISA data. It calculate the Ab/Ag concentration, using the graphical method

::DEVELOPER

G P S Raghavaand J. N. Agrewala

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava G. P. S. and Agrewala J. N. (2001)
A Web Based Method for Computing Endpoint Titer and Concentration of Antibody/Antigen.
Biotech Software and Internet Reports 2(5)196-197

DNASIZE – Computation of size of DNA and Protein Fragments from Their Electrophoretic Mobility

DNASIZE

:: DESCRIPTION

DNASIZE allows to compute the length of DNA or protein fragments from its electropheric mobility using a graphical method.

::DEVELOPER

G P S Raghava

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • DOS

:: DOWNLOAD

  DNASIZE 

:: MORE INFORMATION

Citation

Raghava, G. P. S. (2001)
A web server for computing size of DNA/Protein fragment using graphical method.
Biotech Software and Internet Report 2:198-200.

PHYSICO 2 – Computation of Properties of Protein Sequences

PHYSICO 2

:: DESCRIPTION

PHYSICO2 is an UNIX based Standalone Procedure for Computation of Physicochemical, Window-dependent and Substitution Based Evolutionary Properties of Protein Sequences along with Automated Block Preparation Tools.

::DEVELOPER

PHYSICO team

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PHYSICO

:: MORE INFORMATION

Citation:

PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2.
Banerjee S, Gupta PS, Nayek A, Das S, Sur VP, Seth P, Islam RN, Bandyopadhyay AK.
Bioinformation. 2015 Jul 31;11(7):366-8. doi: 10.6026/97320630011366.

Treekin 0.4 – Computation of RNA Folding Dynamics

Treekin 0.4

:: DESCRIPTION

The program  treekin  computes folding dynamics on coarse grained version of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state.

::DEVELOPER

Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Treekin

:: MORE INFORMATION

Citation

Michael T Wolfinger, W Andreas Svrcek-Seiler, Christoph Flamm, Ivo L Hofacker and Peter F Stadler
Efficient computation of RNA folding dynamics
J. Phys. A: Math. Gen. 37 4731,

DNA Melting 20080207 – Computations on DNA melting

DNA Melting 20080207

:: DESCRIPTION

DNA Melting is a server performs web-based computations on DNA melting, thus predicting the localized separation of the two strands for sequences provided by the users.

::DEVELOPER

Geir Ivar Jerstad, Eivind Tøstesen – eivindto(at)ulrik.uio.no, Eivind Hovig – ehovig(at)ifi.uio.no

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

E. Tøstesen, G. I. Jerstad and E. Hovig (2005)
Stitchprofiles.uio.no: Analysis of partly melted DNA conformations using stitch profiles
Nucl. Acids Res., 33, w573-w576. Doi:10.1093/nar/gki424.

VASCo 1.0.2 – Computation and Visualization of Annotated Protein Surface Contacts

VASCo 1.0.2

:: DESCRIPTION

VASCo is a program pipeline including a visualization tool to calculate and visualize annotated surfaces with special emphasis on surface contact regions and protein-protein interactions. Crystal contacts and biological contacts can be calculated based on surface points. Molecular properties such as electrostatic potential or hydrophobicity can be calculated and mapped on those surface points. The molecular surfaces and properties are calculated using existing established programs, which are integrated into the package, as well as using own developed programs. The modular pipeline can easily be extended to include new properties for annotation. The output of this pipeline is most conveniently displayed in PyMOL as Compiled Graphics Objects (CGO) using a custom-made plug-in.

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Python
  • Mymol

:: DOWNLOAD

 VASCo

:: MORE INFORMATION

Citation

Steinkellner G, Rader R, Thallinger GG, Kratky C, Gruber K.
VASCo: computation and visualization of annotated protein surface contacts
BMC Bioinformatics 2009, 10(1):32

TD 2.0 – Computation of the Transformation Distance for a set of DNA sequences

TD 2.0

:: DESCRIPTION

TD (Transformation Distance) : pairwise compare sequences and reveal segment inversions, duplications.

::DEVELOPER

JS Varré, Eric Rivals

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX / Windows

:: DOWNLOAD

 TD

:: MORE INFORMATION

Citation

JS Varré, JP Delahaye, E Rivals,
Transformation Distances: a family of dissimilarity measures based on movements of segments,
Bioinformatics, vol. 15, no. 3, pp 194-202, 1999.

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