MM2S 1.0.6 – Personalized Diagnosis of Medulloblastoma Subtypes Across Patients and Model Systems

MM2S 1.0.6

:: DESCRIPTION

The MM2S (Medullo-Model To Subtypes) classifier stratifies single MB gene expression profiles without reference samples or replicates. The pathway-centric approach facilitates subtype predictions of patient samples, and model systems including cell lines and mouse models.

::DEVELOPER

Princess Margaret Bioinformatics and Computational Genomics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 MM2S

:: MORE INFORMATION

Citation:

Genomics. 2015 Aug;106(2):96-106. doi: 10.1016/j.ygeno.2015.05.002. Epub 2015 May 12.
Personalized diagnosis of medulloblastoma subtypes across patients and model systems.
Gendoo DM, Smirnov P, Lupien M, Haibe-Kains B

HaploShare 1.02 – Find Shared Haplotypes among Patients from a common recent Ancestor

HaploShare 1.02

:: DESCRIPTION

HaploShare was designed to find shared haplotypes among patients from a common recent ancestor.

::DEVELOPER

WANLING YANG’S GROUP IN BIOINFORMATICSUniversity of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 HaploShare

:: MORE INFORMATION

Citation

Genome Biol. 2015 May 9;16:92. doi: 10.1186/s13059-015-0662-9.
HaploShare: identification of extended haplotypes shared by cases and evaluation against controls.
Ying D, Sham PC, Smith DK, Zhang L, Lau YL, Yang W.

CRCRpred – Webserver for Risk Prediction in Colo-rectal Cancer Patients

CRCRpred

:: DESCRIPTION

CRCRpred (Colo-Rectal Cancer Risk Prediction) webserver can be used to distinguish high risk CRC patients from low risk CRC patients given the protein concentration of one or more apoptotic proteins (Bak, Bax, Bcl2, BclXL or Mcl1) involved in the process of Mitochondrial Outer Membrane Permeabilization (MOMP), which is defunct in the case of cancer. The risk estimation is based on statistical and survival analysis on recent CRC datasets.

::DEVELOPER

CRCRpred team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Prediction of risk scores for colorectal cancer patients from the concentration of proteins involved in mitochondrial apoptotic pathway.
Lathwal A, Arora C, Raghava GPS.
PLoS One. 2019 Sep 9;14(9):e0217527. doi: 10.1371/journal.pone.0217527.

PhenoTips 1.4.7 – Patient Phenotyping software

PhenoTips 1.4.7

:: DESCRIPTION

PhenoTips is an open source software tool for collecting and analyzing phenotypic information for patients with genetic disorders.

::DEVELOPER

Computational Biology Lab at the University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 PhenoTips

:: MORE INFORMATION

Citation:

Hum Mutat. 2013 Aug;34(8):1057-65. doi: 10.1002/humu.22347. Epub 2013 May 24.
PhenoTips: patient phenotyping software for clinical and research use.
Girdea M1, Dumitriu S, Fiume M, Bowdin S, Boycott KM, Chénier S, Chitayat D, Faghfoury H, Meyn MS, Ray PN, So J, Stavropoulos DJ, Brudno M.

PASSIM – The Patient and Sample System for Information Management

PASSIM

:: DESCRIPTION

PASSIM (The Patient and Sample System for Information Management)is an open source software system for managing information in biomedical studies. The data submission form is brief, thus making the system simple to use and customize for any biomedical study easily.
The PASSIM consists of the two parts:

1. Stand-alone Person Management Tool (PMT), used on-site by staff collecting the samples
2. Sample Management Database accessible through the web-based interface

::DEVELOPER

 Institute of Mathematics and Computer Science , EBI.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 PASSIM

:: MORE INFORMATION

Citation:

Viksna J, Celms E, Opmanis M, Podnieks K, Rucevskis P, Zarins A, Barrett A, Neogi SG, Krestyaninova M, McCarthy MI, Brazma A, Sarkans U.
PASSIM – an open source software system for managing information in biomedical studies.
BMC Bioinformatics. 2007 Feb 9;8:52.