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Top Apps

  • Identify and respond to threats before damage is done Identify and respond to threats before damage is done Icon
    Identify and respond to threats before damage is done Icon

    A SIEM that makes it easy to use logs for security, compliance, and troubleshooting.

    SolarWinds® Log & Event Manager (LEM) delivers comprehensive Security Information and Event Management (SIEM) capabilities in a highly affordable, easy-to-use, and quick-to-deploy virtual appliance. LEM provides the visibility, security, and control that IT professionals need to alert on and respond to security threats, and assist in meeting the regulatory compliance guidelines of HIPAA, PCI DSS, SOX, and more. Try it free for 30 days!
  • Multi-vendor storage monitoring simplified Multi-vendor storage monitoring simplified Icon
    Multi-vendor storage monitoring simplified Icon

    Monitor your multi-vendor storage to help ensure your applications get the performance & capacity they need with SolarWinds® Storage Resource Monitor.

    SolarWinds Storage Resource Monitor (SRM) gives you multi-vendor storage performance monitoring and alerting to help ensure peak storage performance. Automated capacity planning helps you predict storage shortages, reclaim space, and prevent application outages. SRM integrates with other Orion® Platform products to provide end-to-end visibility into the application stack, and lets you easily troubleshoot performance issues from application to storage.
  • Virtual Laboratory Environment Icon

    Virtual Laboratory Environment

    A multi-modeling and simulation environment to study complex systems

    VLE is a multi-modeling and simulation environment to study complex dynamic systems. VLE is based on the discrete event specification DEVS. and it implements the DSDE formalism (A merge of Dynamic Structure DEVS, DSDEVS, with Parallel DEVS, PDEVS). VLE provides a complete set of C++ libraries, called VFL (VLE Foundation Libraries), to develop DEVS models, to gets results of simulations, to launch simulation on cluster. The models can be developed with the DEVS formalism or with the classical mathematical formalism: Ordinary Differential Equation with Euler, Range-Kutta or QSS integrator, Finite state automaton (FDDEVS, UML State chart, Hybrid Petri net). The VLE environment provides an IDE to develop C++ models, DEVS coupled models. VLE have also three ports to use the VFL with Python, Java and R programming languages.

  • TXM Icon


    Unicode-XML-TEI text/corpus analysis platform

    TXM is a free and open-source cross-platform Unicode & XML based text/corpus analysis environment and graphical client, supporting Windows, Linux and Mac OS X. It can also be used online as a J2EE standard compliant web portal (GWT based) with access control built in. DOWNLOAD LATEST VERSION OF TXM : TXM offers a comprehensive range of analysis tools (concordances, collocate search, frequency lists, etc.) based on the powerfull CQP full text search engine ( and a range of statistical functions (factorial analysis, classification, cooccurrency analysis, etc.) based on R packages ( Read the scientific background at the Textométrie project web site Read a full description at the TEI Tools wiki

  • Bio7 Icon


    The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.


    Copy Number Analysis for Targeted Resequencing (CONTRA) is a tool for copy number variation (CNV) detection for targeted resequencing data such as those from whole-exome capture data.

    Downloads: 49 This Week Last Update: See Project
  • ncPRO-seq Icon


    Non-Coding RNA PROfiling from sRNA-seq

    ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. ############# Docker version : download and run Dockerfile (go in "Files" section) ############# GitHub :

    Downloads: 37 This Week Last Update: See Project
  • Trial SolarWinds Backup and you could receive a free Amazon Echo Dot Trial SolarWinds Backup and you could receive a free Amazon Echo Dot Icon
    SolarWinds Backup provides lightning-quick recovery that can restore business continuity after a disaster. For a limited time only, when you try SolarWinds Backup and store at least 100GB of selected data, you have the chance to receive a free Amazon Echo Dot.
  • R packages (maintained by YJLEE) Icon

    R packages (maintained by YJLEE)

    R packages for PK/PD modeling, BE/BA, drug stability, ivivc, etc.

    These R packages are developed for data analysis of PK/PD modeling, bioequivalence/bioavailability (BE/BA), drug stability, in-vitro and in-vivo correlation (ivivc), as well as therapeutic drug monitoring (TDM). They include bear, ivivc, PKfit, stab and tdm.

  • BEMoDA

    Bioequivalence Model Dependent-Independent Approach

    Bioequivalence Model Dependent-Independent Approach scripts for in-vitro dissolution profile comparison as proposed by Sathe et al. in 1996 (Sathe PM, Tsong Y, Shah VP. In-vitro dissolution profile comparison: statistics and analysis, model dependent approach. Pharm Res. 1996 Dec;13(12):1799-803) and Tsong et al. in 1996 (Tsong Y, Hammerstrom T, Sathe P, Shah VP. (1996) Statistical Assessment of Mean Differences between Two Dissolution Data Sets, Drug Info. J. 30:1105-1112).

    Downloads: 32 This Week Last Update: See Project
  • RDXplorer

    The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.

  • Cell-ID

    Toolchain for quantification of fluorescence intensity and morphological parameters in single cells using microscope based cytometry.

  • libirt

    The new site is at

    The new site is at Library of functions to estimate the items and abilities from the responses of subjects to a questionnaire. The IRT models supported are the logistic model, the multivariate logistic model, the graded model and smoothing by penalization and kernel.

    Downloads: 12 This Week Last Update: See Project
  • The First VoIP Communications Cloud in the World The First VoIP Communications Cloud in the World Icon
    The First VoIP Communications Cloud in the World Icon

    The Smarter Business Phone Solution

    • Powerful Unified Communication Features
    • Fast, Easy, Free Setup & Install
    • Trusted by 47,000+ Companies in 100 Countries
  • CyberUnits Icon


    Units for computational cybernetics

    CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal, S and Matlab.

    Downloads: 10 This Week Last Update: See Project
  • CABBaGe Icon


    Classification Algorithm Based on a Bayesian method for Genomics

    Downloads: 7 This Week Last Update: See Project
  • Allelome.PRO

    A pipeline to define allele-specific genomic features

    Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here we present Allelome.PRO, an automated userfriendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analysed imprinted expression to give a complete picture of the “allelome” by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased biallelic or noninformative. Allelome.PRO offers increased sensitivity to analyse lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data.

    Downloads: 2 This Week Last Update: See Project
  • Panacea

    PAN And Core-gEnome Analysis

    A tool to calculate the Pan-Genome of a set of annotated genomes

    Downloads: 2 This Week Last Update: See Project
  • YANG J. (Yet Another Network Generator) Icon

    YANG J. (Yet Another Network Generator)

    YANG (Yet Another Network Generator - Java) enables you to generate social networks given various social rules observed in the real population. Uses: generate realistic networks to be used in individual-centric models, teaching or benchmarking.

  • decima

    Decima is a database that was designed to support time-series data mining. It consists of PostgreSQL custom type definition, implementation of GiST index for that type and snowflake database schema.

    Downloads: 2 This Week Last Update: See Project
  • phcfM Icon


    R package for modelling anthropogenic deforestation

    phcfM is an R package for modelling anthropogenic deforestation. It was named after the REDD+ pilot-project 'programme holistique de conservation des forêts à Madagascar'. phcfM includes two main functions: (i) demography(), to model the population growth with time in a hierarchical Bayesian framework using population census data and Gaussian linear mixed models and (ii) deforestation(), to model the deforestation process in a hierarchical Bayesian framework using land-cover change data and Binomial logistic regression models with variable time-intervals between land-cover observations. The two functions use embedded Gibbs samplers written in C++ with the Scythe statistical library to reduce computational time.

    Downloads: 2 This Week Last Update: See Project
  • R Package for the Analysis of DCE-MRI

    A collection of code, bundled into a single R package, to perform several aspects of data management, image pre-processing, data analysis and statistical inference related to the quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI).

    Downloads: 1 This Week Last Update: See Project
  • GNUexp Icon


    GNUexp is a GNUstep/Cocoa framework and a collection of tools helping you to plan, develop, and administer applications associated with visual psychophysics, experimental psychology and statistical data analysis.

    Downloads: 0 This Week Last Update: See Project
  • LD impute

    NGS genotype imputation using LD structure

    Downloads: 0 This Week Last Update: See Project
  • PheMaDB (Phenotype Microarray DataBase)

    PheMaDB is a web-based data management system to store and analyze OmniLog Phenotype Microarray data. The manuscript can be accessed here: Chang WE et al. BMC Bioinformatics. 2011 Apr 20;12(1):109.


    This application allow user to predict dissolution profile of solid dispersion systems based on algorithms like symbolic regression, deep neural networks, random forests or generalized boosted models. Those techniques can be combined to create expert system. Application was created as a part of project K/DSC/004290 subsidy for young researchers from Polish Ministry of Higher Education.

    Downloads: 0 This Week Last Update: See Project
  • SuRankCo

    Supervised Ranking of Contigs in de novo Assemblies

    SuRankCo is a machine learning based software to score and rank contigs from de novo assemblies of next generation sequencing data. It trains with alignments of contigs with known reference genomes and predicts scores and ranking for contigs which have no related reference genome yet. For more details about SuRankCo and its functioning, please see "SuRankCo: Supervised Ranking of Contigs in de novo Assemblies" Mathias Kuhring, Piotr Wojtek Dabrowski, Andreas Nitsche and Bernhard Y. Renard ( PLEASE NOTE, it is recommended to read the paper and the readme.txt file before using SuRankCo. Update Jun2015: * Minor changes to enable BAM support. Update Feb2014: * Added support for FASTA/SAM assemblies in addition to ACE/FASTQ(QUAL). NOTE: features of FASTA/SAM assemblies do not include BaseCount, BaseSeqmentCount and ContigQualities yet.

    Downloads: 0 This Week Last Update: See Project
  • TOPS_CeMM Icon


    User Friendly Data Analysis Tool for Interaction Data

    TOPS provides the benchtop scientist with a free toolset to analyze, filter and visualize data from functional genomic gene-gene and gene-drug interaction screens with a flexible interface to accommodate various different technologies and analysis algorithms in addition to those already provided here.

    Downloads: 0 This Week Last Update: See Project
  • The Protein Similarity Network Icon

    The Protein Similarity Network

    Human protein similarity network used to predict drug safety.

    This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do not hesitate to contact us in the forum or by email. Please see the original manuscript: Lopes, TJS, et al. (2015) - "Identifying problematic drugs based on the characteristics of their targets" - Frontiers in Pharmacology doi: 10.3389/fphar.2015.00186

    Downloads: 0 This Week Last Update: See Project
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