Aug 282014

MendeLIMS 3.2


MendeLIMS is a laboratory information management system (LIMS) that is adaptable to continuously evolving experimental protocols and sequencing technologies. Large clinical genomics studies require the ability to select from a large population of patients/samples to identify the samples of interest. Samples must be accurately tracked through various transformations in order to be certain that DNA sequencing results are attributable to the correct originating sample. This web-based LIMS has a flexible configuration, is easily implemented with open source tools and can be tooled for large scale management of next generation DNA


Ji Research Group




  • MacOsX / Linux
  • Web Server
  • rails 2.3.x and ruby 1.8.7
  • MySQL




Aug 272014
OMSSA 2.1.9 / COMPASS 1.4.1 - MS/MS Peptide Spectra Identification

OMSSA 2.1.9 / COMPASS 1.4.1 :: DESCRIPTION OMSSA [ Open Mass Spectrometry Search Algorithm] is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical method used in BLAST. COMPASS is the Coon [...]

Aug 272014
VPA 0.3.6 - Variant Pattern Analyzer

VPA 0.3.6 :: DESCRIPTION VPA is an R tool for prioritizing variants with specified frequency pattern from multiple study subjects in next-generation sequencing study. ::DEVELOPER Qiang Hu ( :: SCREENSHOTS N/A :: REQUIREMENTS Windows / Linux / Mac OsX R :: DOWNLOAD  VPA :: MORE INFORMATION Citation BMC Res Notes. 2012 Jan 14;5:31. doi: 10.1186/1756-0500-5-31. [...]

Aug 272014
IMA 3.1.2 - High-throughput Analysis of Illumina’s 450K Infinium Methylation data

IMA 3.1.2 :: DESCRIPTION IMA (Illumina Methylation Analyzer) is a package designed to automate the pipeline for analyzing site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray. ::DEVELOPER Dan Wang < > :: SCREENSHOTS N/A :: REQUIREMENTS Windows / Linux / Mac OsX R :: DOWNLOAD  IMA :: MORE INFORMATION [...]

Aug 272014
IQuant 2.0.1 - A pipeline for Quantitative Proteomics based upon Isobaric Tags

IQuant 2.0.1 :: DESCRIPTION IQuant is an automated pipeline for quantitative proteomics based upon isobaric tags. It integrates post-processing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated from the peptides labeled by isobaric tags for quantification. ::DEVELOPER IQuant team :: SCREENSHOTS :: REQUIREMENTS Windows / Linux / Mac OsX [...]

Aug 272014
sapFinder 1.3.1 - Detection of Variant Peptides in Shotgun Proteomics Experiments

sapFinder 1.3.1 :: DESCRIPTION sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics. ::DEVELOPER  Shaohang Xu <xsh.skye at>, Bo Wen <wenbo at> :: SCREENSHOTS N/A :: REQUIREMENTS Windows / Linux / Mac OsX R BioCOnductor :: DOWNLOAD  sapFinder :: MORE INFORMATION [...]

Aug 272014
FARVAT 1.0.10 - FAmily-based Rare Variant Association Test

FARVAT 1.0.10 :: DESCRIPTION FARVAT is a statistical test for gene-based association test with related samples. In addition to FARVAT analyzes large scale genome data in computational efficiency. ::DEVELOPER Won’s laboratory, Seoul National University :: SCREENSHOTS N/A :: REQUIREMENTS Windows / Linux / Mac OsX :: DOWNLOAD  FARVAT :: MORE INFORMATION Citation FARVAT: a family-based [...]

Aug 272014
NAViGaTOR 2.3.0 - Visualize and Analyze Protein-protein Interaction Networks.

NAViGaTOR 2.3.0 :: DESCRIPTION NAViGaTOR (Network Analysis, Visualization, & Graphing TORonto ) is a software package for visualizing and analyzing protein-protein interaction networks.NAViGaTOR can query OPHID / I2D – online databases of interaction data – and display networks in 2D or 3D. To improve scalability and performance, NAViGaTOR combines Java with OpenGL to provide a 2D/3D [...]

Aug 272014
SecureMA 0.2 - Secure Meta-analysis for Genetic Association Studies

SecureMA 0.2 :: DESCRIPTION SecureMA is a secure framework for performing multi-site genetic association studies across large consortia, without violating privacy/confidentiality of individual participants or substudy sites. It aims at addressing various attacks on genomic privacy, and provides comprehensive protection over genomic data without impeding scientific endeavor. ::DEVELOPER Wei Xie ( :: SCREENSHOTS N/A :: [...]

Aug 272014
MethylAid 0.99.6 - Visual and interactive Quality Control of large Illumina 450k data sets

MethylAid 0.99.6 :: DESCRIPTION MethylAid is specially designed for quality control of large sets of DNA methylation data e.g., epigenomewide association studies (EWAS). ::DEVELOPER M. van Iterson <m.van_iterson at> :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Windows/ MacOsX R BioConductor :: DOWNLOAD  MethylAid :: MORE INFORMATION Citation MethylAid: Visual and interactive quality control of [...]