Imaris 8.3 – Analysis, Segmentation and Interpretation of 3D and 4D Microscopy datasets

Imaris 8.3

:: DESCRIPTION

Imaris is Bitplane’s core scientific software module for data visualization, analysis, segmentation and interpretation of 3D and 4D microscopy datasets.

::DEVELOPER

BITPLANE AG

:: SCREENSHOTS

Imaris

:: REQUIREMENTS

  • Windows/MacOsX

:: DOWNLOAD

 Imaris

:: MORE INFORMATION

GMS 20140126 – A Turnkey system for Variant Discovery and Interpretation

GMS 20140126

:: DESCRIPTION

GMS (Genome Model System) is an integrated analysis and information-management system.The system borrows concepts from traditional laboratory information-management systems — such as tracking methods and data-access interfaces, — and applies them to genomic analysis. The result is a standardized system that integrates both analysis and management capabilities.

::DEVELOPER

The Genome Institute at Washington University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • R package

:: DOWNLOAD

  GMS

:: MORE INFORMATION

PeptideShaker 1.1.3 – Interpretation of Proteomics Identifications from multiple search engines

PeptideShaker 1.1.3

:: DESCRIPTION

PeptideShaker is a search engine independent platform for visualization of peptide and protein identification results from multiple search engines.

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux
  • Java

:: DOWNLOAD

 PeptideShaker

:: MORE INFORMATION

Citation

Acta Neurol Scand Suppl. 2012;(195):90-6. doi: 10.1111/ane.12029.
Cerebrospinal fluid proteome comparison between multiple sclerosis patients and controls.
Kroksveen AC, Guldbrandsen A, Vedeler C, Myhr KM, Opsahl JA, Berven FS.

Mutadelic – Goal-driven Patient Variant Annotation and Interpretation

Mutadelic

:: DESCRIPTION

Mutadelic is a tool that analyzes and prioritizes genomic variants by using Description Logic (DL) inferencing to generate workflows which are logically verifiable

::DEVELOPER

Krauthammer Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mutadelic: mutation analysis using description logic inferencing capabilities.
Holford ME, Krauthammer M.
Bioinformatics. 2015 Aug 12. pii: btv467

MAGI – Mutation Annotation & Genome Interpretation

MAGI

:: DESCRIPTION

MAGI is a publicly available web application to explore and annotate cancer genomics data.

::DEVELOPER

Raphael Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

MAGI: visualization and collaborative annotation of genomic aberrations.
Leiserson MD, Gramazio CC, Hu J, Wu HT, Laidlaw DH, Raphael BJ.
Nat Methods. 2015 May 28;12(6):483-4. doi: 10.1038/nmeth.3412.

Synthesis-View – Visualization and Interpretation of SNP Association Results

Synthesis-View

:: DESCRIPTION

Synthesis-View is a data visualization application. Synthesis-View was extended from the previous software “LD-Plus” which also uses a flexible data display format of multiple data “tracks” that can be viewed (Bush, Dudek et al. 2010). Through the use of stacked data-tracks, information on SNP genomic locations, presence of the SNP in a specific study or analysis, as well as related information such as genetic effect size and summary phenotype information, are available for plotting according to user preference.

::DEVELOPER

Ritchie Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Ruby

:: DOWNLOAD

  Synthesis-View

:: MORE INFORMATION

Citation:

Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis.
Pendergrass SA, Dudek SM, Crawford DC, Ritchie MD.
BioData Min. 2010 Dec 16;3:10.

GlycoPeptideSearch 1.3.12 – Interpretation of N-glycopeptide by searching for Glycopeptide Results consistent with MS/MS spectra

GlycoPeptideSearch 1.3.12

:: DESCRIPTION

GlycoPeptideSearch (or GPS) is a siimplifies data interpretation of N-glycopeptide CID MS/MS datasets by searching for glycopeptide results consistent with MS/MS spectra. Results are tabulated in Excel format.

::DEVELOPER

Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 GlycoPeptideSearch

:: MORE INFORMATION

Citation

J Proteome Res. 2012 Mar 2;11(3):1728-40. doi: 10.1021/pr201183w. Epub 2012 Feb 6.
Semi-automated identification of N-Glycopeptides by hydrophilic interaction chromatography, nano-reverse-phase LC-MS/MS, and glycan database search.
Pompach P, Chandler KB, Lan R, Edwards N, Goldman R.

SNPTrack 1.1.0 – SNP & GWAS Data Management, Analysis and Interpretation

SNPTrack 1.1.0

:: DESCRIPTION

SNPTrack stores and organizes study data and provides access to functional information about the SNPs in a study, including information about the genes and proteins containing a SNP and Gene Ontology information and pathway information available for those genes and proteins.

::DEVELOPER

the National Center for Toxicological Research (NCTR).

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 SNPTrack

:: MORE INFORMATION

Citation

Hum Genomics. 2012 Jul 5;6(1):5. doi: 10.1186/1479-7364-6-5.
SNPTrackTM : an integrated bioinformatics system for genetic association studies.
Xu J, Kelly R, Zhou G, Turner SA, Ding D, Harris SC, Hong H, Fang H, Tong W.

ANNIE – Protein Sequence Annotation and Interpretation Environment

ANNIE

:: DESCRIPTION

ANNIE is a comprehensive de novo protein annotation system that integrates a large number of indispensable algorithms used in everyday sequence analytic work.

::DEVELOPER

Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W435-40. doi: 10.1093/nar/gkp254. Epub 2009 Apr 23.
ANNIE: integrated de novo protein sequence annotation.
Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G

DeNovo Pipeline 1.5 – Protein Identification by de novo Interpretation

DeNovo Pipeline 1.5

:: DESCRIPTION

DeNovo Pipeline performes protein identification by de novo interpretation by coupling the PepNovo software for sequencing and the Fasta tool for homology searching.

::DEVELOPER

pappso (Plate-forme d’analyses protéomiques de Paris Sud-Ouest)

:: SCREENSHOTS

denovo_pipeline

:: REQUIREMENTS

  • Windows/ MacOsX / Linux
  • Java

:: DOWNLOAD

 DeNovo Pipeline

:: MORE INFORMATION