Category: File Conversion

KEGG2SBML 1.5.0 – Convert KEGG Pathway Database to SBML

KEGG2SBML 1.5.0

:: DESCRIPTION

KEGG2SBML can convert KEGG (Kyoto Encyclopedia of Genes and Genomes) Pathway database files to SBML using the KEGG LIGAND database. KEGG2SBML’s capabilities are currently limited to converting only KEGG Metabolic Pathway files and not other types of KEGG files.

::DEVELOPER

Akiya Jouraku, Nobuyuki Ohta and Akira Funahashi , Dept. of Biosciences and Informatics at Keio University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

KEGG2SBML

:: MORE INFORMATION

Citations

  1. Converting KEGG pathway database to SBML, Funahashi, A., Jouraku, A., and Kitano, H.
    8th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004).
  2. Converting the KEGG pathway database to SBML, Funahashi, A., Jouraku, A., and Kitano, H.
    5th International Conference on Systems Biology (ICSB 2004), October, 2004.

KEGG2SBML License

SBML2SMW 1.0 – Extract Celldesigner Model to Semantic Mediawiki

SBML2SMW 1.0

:: DESCRIPTION

SBML2SMW allows extracting Celldesigner model information, storing this information to a Semantic Mediawiki server and context-sensitive restoring and integration of this information in a Celldesigner model. The application consists of two parts: The Celldesigner-plugin itself which directly communicates with the Celldesigner and so has access to the Celldesigner models and the Translationserver which receives the extracted information and translates it into Semantic Mediawiki syntax and stores it there.

::DEVELOPER

fluid Operations AG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

SBML2SMW

:: MORE INFORMATION

Code license GNU Lesser General Public License

SBML2SMW: bridging System Biology with semantic web technologies for biomedical knowledge acquisition and hypothesis elicitation
Tobias Mathäß, Peter Haase, Hiroaki Kitano, Luca Toldo. 2nd Workshop of Ontologies in Biomedicine and Life Sciences, OBML2010, Mannheim, Germany.

Import Notes 1.1 – CellDesigner Plugin, Import Notes Data from CSV File

Import Notes 1.1

:: DESCRIPTION

CellDesigner allow developers to supply  Plugins to extend the function of CellDesigner.

Import Notes is used  to import notes data from CSV file.

::DEVELOPER

N/A

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Import Notes

:: MORE INFORMATION

Work in CellDesigner 4.0  and above.

PDBCNS 2.0 – Interconvert Atom Names between PDB & CNS formats

PDBCNS 2.0

:: DESCRIPTION

PDBCNS is a perl script to convert atom names for common amino acids and nucleic acid bases from PDB format to CNS (or XPLOR) style atom names.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

PDBCNS

:: MORE INFORMATION

PDBCNS is free software available under the terms of its own BSD-style license.

Remediator 1.60 – Convert PDB Files between PDBv2.3 & PDBv3.2 Formats

Remediator 1.60

:: DESCRIPTION

Remediator converts PDB files between PDBv2.3 and PDBv3.2 formats. It can accurately and rapidly convert in either direction: old to new OR new to old. Atom records of type ATOM, HETATM, TER, ANISOU, SIGATM, SIGUIJ, and LINK are converted, as are DNA residue names (e.g., A, C, T, G of v2.3 cf. DA, DC, DT, DG of v3.2). Remediator is available as a Perl or Python script. The scripts should work on any type of computing platform, as long as your operating system has the appropriate framework.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

:: DOWNLOAD

Remediator

:: MORE INFORMATION

Remediator uses the remediated Chemical Component Dictionary as its “rosetta stone” for conversion.

Remediator is free software available under the terms of its own BSD-style license.

KinImmerse 0.5 – Translate Kinemage Files into Software for Virtual Environment

KinImmerse 0.5

:: DESCRIPTION

KinImmerse translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE.

In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows /  Linux

:: DOWNLOAD

KinImmerse

:: MORE INFORMATION

For a detailed description see KinImmerse: Macromolecular VR for NMR ensembles.

KinImmerse is free software available under the terms of its own BSD-style license.

Prekin 6.51 – Prepares Kinemages Files from PDB-format Files

Prekin 6.51

:: DESCRIPTION

Prekin prepares molecular kinemages (input files for Mage & KiNG) from PDB-format coordinate files, using either a choice of built-in scripts or a flexible user specification of options. Prekin can be run in either an interactive mode with option selection from dialog panes; or, it can be run in command-line fashion with all options specified at program invocation.

::DEVELOPER

Richardson Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

Prekin

:: MORE INFORMATION

Prekin is free software available under the terms of its own BSD-style license.

PovChem 2.1.1 – Chemical Visualization & Illustration & POV File Converter

PovChem 2.1.1

:: DESCRIPTION

PovChem is a chemical visualization and illustration program with a new graphic interface. It takes molecules in the PDB format, lets you to set up a picture with fine control over details of the illustration – colors, atom and bond radii, view orientation, etc. It will even calculate and display hydrogen bonds.

PovChem can export the picture in POV-Ray format, which allows you to render the image with a state-of-the-art raytracer, giving high-quality images at any resolution, for anything from web page thumbnails to full-size high-resolution images for journal covers, advertisements, posters, anything!

::DEVELOPER

Paul A. Thiessen

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

PovChem

:: MORE INFORMATION

PovChem is now free!Use this key to register your copy of PovChem:
APyUrblJnYZr

REDUCK 1.0 – Remove Duplicates

REDUCK 1.0

:: DESCRIPTION

REDUCK removes duplicate lines from a PCL file. Actually, it removes duplicate lines from any text file, but was intended for use with PCL files. Does exactly what it says; if the lines are not 100% identical, they are not removed.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac Os / Linux
  • Perl
  • TK

:: DOWNLOAD

REDUCK for Win ; Source Code

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.

GODACK 1.0 – Good Data

GODACK 1.0

:: DESCRIPTION

GODACK is a simple filtering tool which demands that a certain percentage of datapoints be present in a PCL file. Spots which fail to contain the user-specified percentage of good data points are removed from the dataset.

::DEVELOPER

Falkow Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac Os / Linux
  • Perl
  • TK

:: DOWNLOAD

GODACK for Win ; Source Code

:: MORE INFORMATION

The software is copyrighted under the terms of the GNU General Public License. You can view this license at http://www.gnu.org/licenses/gpl.txt.

Exit mobile version