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http://www.bork.embl.de/j/

The main focus of this Computational Biology group is to predict function and to gain insights into evolution by comparative analysis of complex molecular data. The group currently works on three different scales: * genes and proteins, * protein networks and cellular processes, and * phenotypes and environments. They require both tool development and applications. Some selected projects include comparative gene, genome and metagenome analysis, mapping interactions to proteins and pathways as well as the study of temporal and spatial protein network aspects. All are geared towards the bridging of genotype and phenotype through a better understanding of molecular and cellular processes. The services - resources & tools, developed by Bork Group, are mainly designed and maintained for research & academic purposes. Most of services are published and documented in one or more papers. All our tools can be completely customized and integrated into your existing framework. This service is provided by the company biobyte solutions GmbH. Please visit their tools and services pages for full details and more information. Standard commercial licenses for our tools are also available through biobyte solutions GmbH. The group is partially associated with Max Delbr��ck Center for Molecular Medicine (MDC), Berlin.

Proper citation: EMBL - Bork Group (RRID:SCR_000810) Copy   

•   Source: SciCrunch Registry

http://www.hedtags.org/

Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging.

Proper citation: HED Tags (RRID:SCR_014074) Copy   

•   Source: SciCrunch Registry

https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view

Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences.

Proper citation: Skyline (RRID:SCR_014080) Copy   

•   Source: SciCrunch Registry

http://www.originlab.com/index.aspx?go=PRODUCTS/Origin

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing.

Proper citation: Origin (RRID:SCR_014212) Copy   

•   Source: SciCrunch Registry

http://www.maplesoft.com/products/Maple/

Mathematical software that can compute both numeric and symbolic solutions. It can be used to analyze, explore, visualize, and solve mathematical problems.

Proper citation: Maple (RRID:SCR_014449) Copy   

•   Source: SciCrunch Registry

https://www.wolfram.com/mathematica/

A technical computing software and computing environment that provides users with algorithms and mathematical functions for various projects and purposes. The resource incorporates other Wolfram products such as Wolfram Algorithmbase, Wolfram Language, and Wolfram Knowledgebase.

Proper citation: Wolfram Mathematica (RRID:SCR_014448) Copy   

•   Source: SciCrunch Registry

http://www.kitware.com/opensource/volview.html

A software for volume visualization that can be used by researchers to explore and analyze medical and scientific data. This software uses a variety of tools to load and visualize the data on either a 2D or 3D display. Theses tools include volume rendering, maximum intensity projections and oblique reformatting. Visualizations can be saved mid-session and be reopened at a later time.

Proper citation: VolView (RRID:SCR_014569) Copy   

•   Source: SciCrunch Registry

http://factominer.free.fr/index.html

Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables.

Proper citation: FactoMineR (RRID:SCR_014602) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.

Proper citation: FastQC (RRID:SCR_014583) Copy   

•   Source: SciCrunch Registry

http://www.plexon.com/products/omniplex-software

Neural data acquisition software for signal visualization in neuron recordings along with spike wave-form classification methods. It is made up of the PlexControl software program and the OmniPlex Server.

Proper citation: OmniPlex Software (RRID:SCR_014803) Copy   

•   Source: SciCrunch Registry

http://www.compudrug.com/metabolexpert

Software tool for initial estimation of the structural formula of metabolites, which might be formed by a substance in humans, animals or in plants. MetabolExpert is also capable of predicting the most common metabolic pathways in animals, exporting results to SDF and RDF format and graphical highlighting that empasizes the essence of metabolic reactions that occurred.

Proper citation: MetabolExpert (RRID:SCR_014908) Copy   

•   Source: SciCrunch Registry

http://www.sbpdiscovery.org/technology/sr/bioinformatics/Pages/LaJolla_BioinformaticsandDataManagement.aspx

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 11132025. Facility that provides database development and management and bioinformatic network building services by utilizing on-site hardware and software. Three members of the facility are available to assist researchers with advanced bioinformatics and biostatistics analysis to help put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with the team statistician.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility (RRID:SCR_014868) Copy   

•   Source: SciCrunch Registry

http://www.leadscope.com

Commercial developer of database and predictive model software tools used in chemical toxicity assessment.

Proper citation: Leadscope (RRID:SCR_014904) Copy   

•   Source: SciCrunch Registry

http://netpyne.org/

Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks.

Proper citation: NetPyNE (RRID:SCR_014758) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.

Proper citation: Bowtie 2 (RRID:SCR_016368) Copy   

•   Source: SciCrunch Registry

https://aceabio.com/product/rtca-dp/

Data acquisition and analysis software used for xCELLigence Real Time Cell Analysis SP, DP and MP instruments. The software is used to program and execute experiments and analyze data.

Proper citation: RTCA Software (RRID:SCR_014821) Copy   

•   Source: SciCrunch Registry

https://github.com/macs3-project/MACS

Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.

Proper citation: MACS (RRID:SCR_013291) Copy   

•   Source: SciCrunch Registry

http://www.mrc-lmb.cam.ac.uk/genomes/dolop/

DOLOP is an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. This website along will have additional information on the biosynthetic pathway, supplementary material and other related figures. DOLOP also contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. Additionally, the website features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins.

Proper citation: DOLOP: A Database of Bacterial Lipoproteins (RRID:SCR_013487) Copy   

•   Source: SciCrunch Registry

http://www.cma.mgh.harvard.edu/iatr/display.php?spec=id&ids=107

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. EMMA (Extensible MATLAB Medical image Analysis) is a toolkit designed to ease the use of MATLAB in the analysis of medical imaging data. It provides functions for reading and writing MINC files, viewing images, performing ROI operations, and performing several popular analyses. Also, there are toolkits for performing kinetic analysis of dynamic PET rCBF (regional cerebral blood flow) and FDG data. The goal for this site is to provide a centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools that are of use to the general community.

Proper citation: Extensible MATLAB Medical image Analysis (RRID:SCR_013499) Copy   

•   Source: SciCrunch Registry

http://www.licor.com/bio/products/software/image_studio_lite/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2023. Software application which can analyze basic Western blot data and export them for use in spreadsheet programs. Users can create standardized or custom lab reports and can share them with colleagues. Image Studio Lite has been discontinued and replaced with Empiria Studio Software.

Proper citation: Image Studio Lite (RRID:SCR_013715) Copy   

•   Source: SciCrunch Registry