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http://accelrys.com/products/collaborative-science/biovia-pipeline-pilot/
Software used to automate the process of accessing, analyzing and reporting scientific data. This software can be used by a person with little or no software development experience can create scientific protocols that can be executed through a variety of interfaces including: BIOVIA Web Port, other BIOVIA solutions such as BIOVIA Electronic Lab Notebook, Isentris, Chemical Registration and third-party applications such as Microsoft SharePoint. The protocols aggregate and provide immediate access to volumes of research data, they automate the scientific analysis of data and allow researchers to explore, visualize and report results.
Proper citation: Pipeline Pilot (RRID:SCR_014917) Copy
http://ikrsrv1.medma.uni-heidelberg.de/redmine/projects/ummperfusion
Analysis software for dynamic contrast enhanced magnetic resonance images with implementation of a pixel-by-pixel deconvolution approach. It quantifies T1-weighted contrast-enhanced dynamic MR imaging (DCE-MRI) perfusion data as an OsiriX plug-in.
Proper citation: UMMPerfusion (RRID:SCR_015970) Copy
Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).
Proper citation: FreeContact (RRID:SCR_016113) Copy
https://github.com/broadinstitute/pilon/
Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.
Proper citation: Pilon (RRID:SCR_014731) Copy
http://hms-dbmi.github.io/scde/index.html
Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.)
Proper citation: SCDE (RRID:SCR_015952) Copy
Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.
Proper citation: Brain Imaging Analysis Kit (RRID:SCR_014824) Copy
https://github.com/xavierdidelot/clonalorigin
Software package for comparative analysis of the sequences of a sample of bacterial genomes in order to reconstruct the recombination events that have taken place in their ancestry.
Proper citation: ClonalOrigin (RRID:SCR_016061) Copy
https://sanger-pathogens.github.io/Roary/
Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.
Proper citation: Roary (RRID:SCR_018172) Copy
http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/MrDiffusion
Software package for diffusion imaging analysis and visualization. Module of Vistasoft for processing diffusion weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, RGB fiber direction maps and analysis of MRI data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MrDiffusion (RRID:SCR_016567) Copy
Interactive scientific development environment package for Python. Used for editing, analysis, debugging, and profiling functionality of comprehensive development tool with data exploration, interactive execution, deep inspection, and visualization.
Proper citation: Spyder (RRID:SCR_017585) Copy
Consortium to unite efforts and resources from experts across globe to advance effective, antibody based therapies against novel coronavirus, SARS-CoV-2. Represents multidisciplinary convergence of structural biology, virologists, immunologists, clinicians and bioinformaticians from academic and industry settings. Collects antibodies for testing as part of CoVICS. Contributed antibodies are blinded and will only be known as code name. Antibody contributors will be able to see performance of their own molecules and take part in analysis. Contributors retain ownership of their antibodies and may continue to publish on them using original antibody names. Goal is to determine relative in vitro potency and in vivo efficacy using centralized standardized assays to identify best individual mAbs and rational combinations of mAbs. Consortium will recommend ideal therapeutic molecules for human use to protect vulnerable populations from COVID-19 disease. CoVIC database (CoVIC-DB) will serve as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them.
Proper citation: Coronavirus Immunotherapy Consortium (RRID:SCR_018258) Copy
http://www.uimcimes.es/contenidos/golink?p=1
Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.
Proper citation: QModeling (RRID:SCR_016358) Copy
https://cran.r-project.org/web/packages/geomorph/index.html
Software package for performing all stages of geometric morphometric shape analysis of landmark points and curves in 2-and-3-dimensions as well as 3D surfaces in the R statistical computing environment.
Proper citation: geomorph (RRID:SCR_016482) Copy
http://bioinformatics.uni-muenster.de/tools/nanopipe2
Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms.
Proper citation: NanoPipe (RRID:SCR_016852) Copy
https://www.uke.de/english/research/core-facilities/bioinformatics-core-en.html
Core provides bioinformatics services for researchers at University Medical Center Hamburg Eppendorf and related institutions. Focusing on high throughput sequencing data. Services include data analysis, consulting, software development, and bioinformatical training.
Proper citation: University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility (RRID:SCR_017144) Copy
Web tool for protein-protein docking. Server provides removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering data, and location of heparin-binding sites. Six different energy functions can be used, depending on protein type.This protocol describes use of various options, construction of auxiliary restraints files, selection of energy parameters, and analysis of results.
Proper citation: ClusPro (RRID:SCR_018248) Copy
http://brainarchitecture.org/allen-atlas-brain-toolbox
Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain.
Proper citation: Brain Gene Expression Analysis toolbox (RRID:SCR_017438) Copy
https://covic.lji.org/databases/
Serves as clearinghouse for monoclonal antibodies against SARS-CoV-2. Database will catalog contributed antibodies in searchable resource and provide interactive analysis tools for comparisons among them. Most potent antibodies will guide development of vaccines to stop current outbreak and protect against future pandemics.
Proper citation: CoVIC-DB Database (RRID:SCR_018339) Copy
http://www.rad.upenn.edu/sbia/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 2, 2023. A section of the Penn department of radiology, it is devoted to the development of computer-based image analysis methods and their application to clinical research studies. Image analysis methodologies include image registration, segmentation, population-based statistical analysis, biophysical modeling of anatomical deformations, and high-dimensional pattern classification. Clinical research studies spans a variety of clinical areas and organs, and they include brain diseases such as Alzheimer's disease and schizophrenia, evaluation of treatment effects in large clinical trials, diagnosis of cardiac diseases, and diagnosis prostate, breast and brain cancer. SBIA also performs small animal imaging research aiming to understand brain development in mouse models. It has multiple resources which can be accessed by researcher.
Proper citation: SBIA (RRID:SCR_013628) Copy
Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types.
Proper citation: CellProfiler Image Analysis Software (RRID:SCR_007358) Copy
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