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http://services.bio.ifi.lmu.de/ProSAS
This database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several Ensembl genomes and alternative transcripts can be analyzed on the protein structure and protein function level using the intuitive user interface of the database. Users can search based on Ensembl gene or Ensembl transcript ids, Gene descriptions, Uniprot gene names, Genes matching patterns, Swissprot/Uniprot identifiers or Affymetrix probeset ids.
Proper citation: ProSAS (RRID:SCR_007876) Copy
Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License. Because of the overwhelming success of the first open movie project, Ton Roosendaal, the Blender Foundation''s chairman, has established the Blender Institute. This now is the permanent office and studio to more efficiently organize the Blender Foundation goals, but especially to coordinate and facilitate Open Projects related to 3D movies, games or visual effects.
Proper citation: Blender (RRID:SCR_008606) Copy
Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. Google Scholar helps you find relevant work across the world of scholarly research. Features of Google Scholar * Search diverse sources from one convenient place * Find articles, theses, books, abstracts or court opinions * Locate the complete document through your library or on the web * Learn about key scholarly literature in any area of research How are documents ranked? Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature. * Publishers - Include your publications in Google Scholar * Librarians - Help patrons discover your library''s resources
Proper citation: Google Scholar (RRID:SCR_008878) Copy
http://srv00.recas.ba.infn.it/ASPicDB/
A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation.
Proper citation: ASPicDB (RRID:SCR_002102) Copy
http://support.illumina.com/sequencing/sequencing_software/casava.html
Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting
Proper citation: CASAVA (RRID:SCR_001802) Copy
A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console.
Proper citation: SciPy (RRID:SCR_008058) Copy
http://www.broadinstitute.org/mammals/haploreg/haploreg.php
HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.
Proper citation: HaploReg (RRID:SCR_006796) Copy
Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: ImageQuant (RRID:SCR_014246) Copy
https://pathcore.bsd.uchicago.edu/Downloads/HTRC_ImageScUG.pdf
Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: ImageScope (RRID:SCR_014311) Copy
Platform for quantitative and qualitative proteomics research for Waters Corporation proteomics systems.
Proper citation: ProteinLynx Global Server (RRID:SCR_016664) Copy
https://www.schrodinger.com/maestro
Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data.
Proper citation: Maestro (RRID:SCR_016748) Copy
http://www.cb.uu.se/~amin/BlobFinder/
Software that can perform calculations on cells from fluorescence microscopy images. BlobFinder can perform two types of analysis: an average count analysis to count the number of fluorescent signals and nuclei in an image, and a single cell analysis to simulate a cytoplasm and assign each signal to a particular cell.
Proper citation: BlobFinder (RRID:SCR_015788) Copy
https://www.embl-hamburg.de/biosaxs/software.html
Software toolkit for small-angle scattering data analysis from biological macromolecules.
Proper citation: ATSAS (RRID:SCR_015648) Copy
https://www.phenix-online.org/documentation/reference/refinement.html
Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB.
Proper citation: Phenix.refine (RRID:SCR_016736) Copy
https://www.indicalab.com/halo/
Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology.
Proper citation: HALO (RRID:SCR_018350) Copy
https://github.com/Tarskin/LaCyTools
Software high throughput data extraction package for LC-MS data.Targeted Liquid Chromatography-Mass Spectrometry data processing package for relative quantitation of glycopeptides.
Proper citation: LaCyTools (RRID:SCR_024525) Copy
https://CRAN.R-project.org/package=GOplot
Software R package for visually combining expression data with functional analysis.
Proper citation: GOplot (RRID:SCR_024419) Copy
https://CRAN.R-project.org/package=geepack
Software R package implements generalized estimating equations for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can handle clustered categorical responses. Used for fitting marginal generalized linear models to clustered data.
Proper citation: geepack (RRID:SCR_024510) Copy
https://cran.r-project.org/web/packages/dagitty/
Software R package provides access to all of the capabilities of DAGitty web application for drawing and analysing Directed Acyclic Graphs within the R platform for statistical computing. Used for graphical analysis of structural causal models.
Proper citation: DAGitty (RRID:SCR_024509) Copy
https://github.com/ekmolloy/fastmulrfs
Software pipeline for estimating species trees from multi copy gene trees.
Proper citation: FastMulRFS (RRID:SCR_024505) Copy
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