CSML2SBML – Converting Quantitative Biological Pathway Models from CSML into SBML

CSML2SBML

:: DESCRIPTION

CSML2SBML is a format convertor for quantitative biological pathways,  converting models expressed in CSML into SBML, enabling simulations or parameter estimation with compliant tools such as CellDesigner and COPASI

::DEVELOPER

CSML2SBML team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 CSML2SBML

:: MORE INFORMATION

Citation

CSML2SBML: A novel tool for converting quantitative biological pathway models from CSML into SBML.
Li C, Nagasaki M, Ikeda E, Sekiya Y, Miyano S.
Biosystems. 2014 Jul;121:22-8. doi: 10.1016/j.biosystems.2014.05.004.

CrossMap 0.5.3 – Convert Genome Coordinates Between Assemblies

CrossMap 0.5.3

:: DESCRIPTION

CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies.

::DEVELOPER

CrossMap team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Python
  • C++ Compiler

:: DOWNLOAD

  CrossMap

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Apr 1;30(7):1006-7. doi: 10.1093/bioinformatics/btt730. Epub 2013 Dec 18.
CrossMap: a versatile tool for coordinate conversion between genome assemblies.
Zhao H1, Sun Z, Wang J, Huang H, Kocher JP, Wang L.

smallWig – Parallel Compression of RNA-seq WIG Files

smallWig

:: DESCRIPTION

The smallWig tool provides compression/decompression for WIG files.

::DEVELOPER

Zhiying WangTsachy (Itschak) Weissman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

  smallWig

:: MORE INFORMATION

Citation

smallWig: Parallel Compression of RNA-seq WIG Files.
Wang Z, Weissman T, Milenkovic O.
Bioinformatics. 2015 Sep 30. pii: btv561.

VCF-Miner 4.0.1 – Analysis of VCF files

VCF-Miner 4.0.1

:: DESCRIPTION

VCF-Miner is a graphical user interface for sorting, filtering and querying information encoded in VCF (Variant Call Format) files.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 VCF-Miner

:: MORE INFORMATION

Citation

VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files.
Hart SN, Duffy P, Quest DJ, Hossain A, Meiners MA, Kocher JP.
Brief Bioinform. 2016 Mar;17(2):346-51. doi: 10.1093/bib/bbv051.

RTCGAToolbox 2.21.5 – Exporting TCGA Firehose Data

RTCGAToolbox 2.21.5

:: DESCRIPTION

RTCGAToolbox is an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for further data analysis.

::DEVELOPER

Mehmet Kemal Samur

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

RTCGAToolbox 

:: MORE INFORMATION

Citation

Samur MK.
RTCGAToolbox: a new tool for exporting TCGA Firehose data.
PLoS One. 2014 Sep 2;9(9):e106397. doi: 10.1371/journal.pone.0106397. PMID: 25181531; PMCID: PMC4152273.

GEO2Enrichr – Browser Extension for Extracting Differentially Expressed Gene Sets from GEO

GEO2Enrichr

:: DESCRIPTION

GEO2Enrichr is web application and two browser extensions (one for Chrome and another for Firefox) designed to facilitate the extraction of signatures from studies posted on the Gene Expression Omnibus (GEO) database.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Chrome / Firefox

:: DOWNLOAD

GEO2Enrichr

:: MORE INFORMATION

Citation

Bioinformatics. 2015 Sep 15;31(18):3060-2. doi: 10.1093/bioinformatics/btv297. Epub 2015 May 13.
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions.
Gundersen GW, Jones MR, Rouillard AD, Kou Y, Monteiro CD, Feldmann AS, Hu KS, Ma’ayan A.

Sig2BioPAX v4 – Java tool for Converting Flat Text files to BioPAX Level 3 format

Sig2BioPAX v4

:: DESCRIPTION

Sig2BioPAX is a Java program that can be used to convert structured text files describing molecular interactions into the BioPAX Level 3 standard format.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 Sig2BioPAX

:: MORE INFORMATION

Citation

Source Code Biol Med. 2011 Mar 21;6:5. doi: 10.1186/1751-0473-6-5.
Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format.
Webb RL, Ma’ayan A.