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http://hippocampome.org

A curated knowledge base of the circuitry of the hippocampus of normal adult, or adolescent, rodents at the mesoscopic level of neuronal types. Knowledge concerning dentate gyrus, CA3, CA2, CA1, subiculum, and entorhinal cortex is distilled from published evidence and is continuously updated as new information becomes available. Each reported neuronal property is documented with a pointer to, and excerpt from, relevant published evidence, such as citation quotes or illustrations. Please note: This is an alpha-testing site. The content is still being vetted for accuracy and has not yet undergone peer-review. As such, it may contain inaccuracies and should not (yet) be trusted as a scholarly resource. The content does not yet appear uniformly across all combinations of browsers and screen resolutions.

Proper citation: Hippocampome.org (RRID:SCR_009023) Copy   

•   Source: SciCrunch Registry
  

http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=lncBase/index

Database that hosts elaborated information for both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA and lncRNA related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. The Prediction Module, which is based on the latest version of DIANA-microT target prediction algorithm (DIANA-microT-CDS), contains detailed information for more than 10 million interactions, between 56,097 lncRNAs and 3,078 miRNAs, ranging from miRNA and lncRNA related details to specific information regarding their interaction sites, graphical representation of their binding and the predicted score. This module exhibits a unique feature for searching the database. Users are able to add genomic locations to their queries thus browsing every miRNA-lncRNA interaction that has at least one MRE located inside the queried locus.

Proper citation: DIANA-LncBase (RRID:SCR_010840) Copy   

•   Source: SciCrunch Registry
  

http://www.acedb.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software genome database management system.

Proper citation: AceDB (RRID:SCR_010671) Copy   

•   Source: SciCrunch Registry
  

http://race.unil.ch/

A collection of web tools designed to assist with the analysis of DNA microarray data and results. RACE performs probe level data preprocessing, quality checks, normalization, and visualization for Affymetrix GeneChips. In addition, it performs clustering and differential analysis of normalized expression levels or ratios for arbitrary platforms, and estimates the false discovery rates in lists of potentially regulated genes. A Gene Ontology (GO)-term analysis assists in the biological interpretation of gene lists. The user can customize each analysis request; upon submission the analysis is executed in a fully automated way., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RACE (RRID:SCR_010950) Copy   

•   Source: SciCrunch Registry
  

http://159.149.160.51/pscan_chip_dev/

Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria.

Proper citation: Pscan-ChIP (RRID:SCR_010885) Copy   

•   Source: SciCrunch Registry
  

http://cupsat.tu-bs.de/

A tool to predict changes in protein stability upon point mutations.

Proper citation: CUPSAT (RRID:SCR_010773) Copy   

•   Source: SciCrunch Registry
  

http://ls-snp.icm.jhu.edu/ls-snp-pdb/

A web tool for genome-wide annotation of human SNPs.

Proper citation: LS-SNP/PDB (RRID:SCR_010774) Copy   

•   Source: SciCrunch Registry
  

http://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml

VAST is a computer algorithm developed at NCBI and used to identify similar protein 3-dimensional structures by purely geometric criteria, and to identify distant homologs that cannot be recognized by sequence comparison. Related structures for every structure in MMDB are pre-computed using VAST and accessible via links on the MMDB Structure Summary pages. The VAST Search page also allows you to compare the coordinates of a newly resolved structure in PDB format against all structures in MMDB to find its neighbors. Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one. From the MMDB Structure summary pages, retrieved via Entrez, structure neighbors are available for protein chains and individual structural domains. If you already know a PDB/MMDB-Id you can try this at once, using the input form in the right column. VAST Search is a service that allows searching for structural neighbors starting with a set of 3D-coordinates specified by the user. This service is meant to be used with newly determined protein structures that are not yet part of MMDB. Structure neighbors for proteins already in MMDB have been pre-computed and can simply be looked up from MMDB''s Structure summary pages!

Proper citation: Vector Alignment Search Tool (RRID:SCR_010655) Copy   

•   Source: SciCrunch Registry
  

http://plantgrn.noble.org/PlantTFcat/

A web-based analysis tool that is designed to identify and categorize plant TF/TR/CR genes from genome-scale protein and nucleic acid sequences by systematically analyzing InterProScan domain patterns in protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PlantTFcat (RRID:SCR_010898) Copy   

•   Source: SciCrunch Registry
  

http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl

A flexible tool for visualizing and analyzing your two-colour microarray slides.

Proper citation: ArrayPipe (RRID:SCR_010934) Copy   

•   Source: SciCrunch Registry
  

https://github.com/telatin/covtobed

Software tool to generate BED coverage tracks from BAM files.

Proper citation: covtobed (RRID:SCR_023998) Copy   

•   Source: SciCrunch Registry
  

http://bioinfo.unl.edu/gramalign.php

Software tool as time efficient progressive Multiple Sequence Alignment algorithm. Sequence distance estimation step is determined by the natural grammar present in nucleotide and amino acid sequences.

Proper citation: GramAlign (RRID:SCR_024032) Copy   

•   Source: SciCrunch Registry
  

https://gitlab.com/rki_bioinformatics/IDeFIX

Software tool for demultiplexing Illumina NGS data. Reports inconsistencies between the raw data and the Sample Sheet, checks for duplicates of indices/ index combinations in the latter and removes unwanted characters from it. Creates an IDeFIX_Report.csv containing the indices/ index combinations from the raw data and their abundance as well as their count in the Sample Sheet and the corresponding Index ID(s).

Proper citation: IDeFIX (RRID:SCR_024033) Copy   

•   Source: SciCrunch Registry
  

https://github.com/lbcb-sci/graphmap2

Software tool as splice aware RNA-seq mapper for long reads produced by Pacific Biosciences and Oxford Nanopore devices

Proper citation: GraphMap2 (RRID:SCR_024035) Copy   

•   Source: SciCrunch Registry
  

https://github.com/genouest/biomaj

Software workflow engine dedicated to data synchronization and processing. Software automates the update cycle and the supervision of the locally mirrored databank repository.

Proper citation: BioMAJ (RRID:SCR_023983) Copy   

•   Source: SciCrunch Registry
  

https://www.gnumed.de/documentation/

Software to build Electronic Medical Record in multiple languages to assist and improve longitudinal care specifically in ambulatory settings.Useful to anyone documenting the health of patients including,doctors, physical therapists, occupational therapists,acupuncturists, nurses, psychologists.

Proper citation: GNUmed (RRID:SCR_024029) Copy   

•   Source: SciCrunch Registry
  

http://ruby.chemie.uni-freiburg.de/~martin/chemtool/

Software tool for drawing organic molecules. Runs under the X Window System using the GTK widget set. Used for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.

Proper citation: Chemtool (RRID:SCR_023992) Copy   

•   Source: SciCrunch Registry
  

http://www.biolchem.ucla.edu/labs/ernst/ChromImpute/

Software tool for large scale systematic epigenome imputation. ChromImpute takes existing compendium of epigenomic data and uses it to predict signal tracks for mark-sample combinations not experimentally mapped or to generate a potentially more robust version of data sets that have been mapped experimentally.

Proper citation: ChromImpute (RRID:SCR_023990) Copy   

•   Source: SciCrunch Registry
  

https://itk.org/

Open source, software cross-platform library that provides suite of software tools for image analysis.ITK builds on proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.

Proper citation: Insight Toolkit (RRID:SCR_024040) Copy   

•   Source: SciCrunch Registry
  

https://github.com/HadrienG/InSilicoSeq

Software tool as sequencing simulator producing realistic Illumina reads. Primarily intended for simulating metagenomic samples, it can also be used to produce sequencing data from a single genome.

Proper citation: InSilicoSeq (RRID:SCR_024041) Copy   

•   Source: SciCrunch Registry