Tools   Select Another Resource Report Type

http://www.ddbj.nig.ac.jp

Maintains and provides archival, retrieval and analytical resources for biological information. Central DDBJ resource consists of public, open-access nucleotide sequence databases including raw sequence reads, assembly information and functional annotation. Database content is exchanged with EBI and NCBI within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). In 2011, DDBJ launched two new resources: DDBJ Omics Archive and BioProject. DOR is archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between the ArrayExpress at EBI and DOR in the common MAGE-TAB format. BioProject provides organizational framework to access metadata about research projects and data from projects that are deposited into different databases.

Proper citation: DNA DataBank of Japan (DDBJ) (RRID:SCR_002359) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/genome

Database that organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations in six major organism groups: Archaea, Bacteria, Eukaryotes, Viruses, Viroids, and Plasmids. Genomes of over 1,200 organisms can be found in this database, representing both completely sequenced organisms and those for which sequencing is in progress. Users can browse by organism, and view genome maps and protein clusters. Links to other prokaryotic and archaeal genome projects, as well as BLAST tools and access to the rest of the NCBI online resources are available.

Proper citation: NCBI Genome (RRID:SCR_002474) Copy   

•   Source: SciCrunch Registry

https://github.com/seqan/seqan/tree/master/apps/mason2

Collection of software tools for simulating biological sequences, including simulations of genome fragment sampling, random genomic sequences, methylation levels, and NGS reads.

Proper citation: Mason (RRID:SCR_002476) Copy   

•   Source: SciCrunch Registry

http://www.med.unc.edu/bric/ideagroup/free-softwares/libra-longitudinal-infant-brain-processing-package

A toolbox with graphical user interfaces for processing infant brain MR images. Longitudinal (or single-time-point) multimodality (including T1, T2, and FA) (or single-modality) data can be processed using the toolbox. Main functions of the software (step by step) include image preprocessing, brain extraction, tissue segmentation and brain labeling. Linux operating system (64 bit) is required. A workstation or server with memory >8G is recommended for processing many images simutaneously. The graphical user interfaces and overall framework of the software are implemented in MATLAB. The image processing functions are implemented with the combination of C/C++, MATLAB, Perl and Shell languages. Parallelization technologies are used in the software to speed up image processing.

Proper citation: iBEAT (RRID:SCR_002470) Copy   

•   Source: SciCrunch Registry

http://brainmeta.com/connectivity_cortical_references_web.php

Bibliography for primate cortical connectivity. The page displays the articles by their year of publication and links to PubMed.

Proper citation: Primate Cortical Connectivity Database (RRID:SCR_002468) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/se/plink/

Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: pFind Studio: pLink (RRID:SCR_000084) Copy   

•   Source: SciCrunch Registry

http://www.tm4.org/spotfinder.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression.

Proper citation: Spotfinder (RRID:SCR_000085) Copy   

•   Source: SciCrunch Registry

http://sarahcannonresearch.com/

A global cancer institute of the Hospital Corporation of America which offers integrated cancer services with access to current therapies.

Proper citation: Sarah Cannon Research Institute; Tennessee; USA (RRID:SCR_000003) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ontologyviz/

Software that allows user to do faceted search on an ontology and enables visualization of the search results on the 3D digital atlas. Currently supports faceted search of functional neuroanatomy.

Proper citation: Faceted Search Based Ontology Visualizer (RRID:SCR_000124) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.nyu.edu/Projects/GOALIE/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Generalized Ontological Algorithmic Logical Invariants Extractor (GOALIE) is a tool for the construction of time-course dependent enrichments. Requires an ODBC connection to an instance of the GO database. Platform: Windows compatible, Mac OS X compatible, Linux compatible

Proper citation: GOALIE (RRID:SCR_000088) Copy   

•   Source: SciCrunch Registry

http://www.computationalbioenergy.org/parallel-meta.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Open source pipeline for metagenomic data analysis, which enables efficient and parallel analysis of multiple metagenomic datasets and visualization of results for multiple samples. Can perform rapid data mining among microbial community data for comparative taxonomic and functional analysis.

Proper citation: Parallel-META (RRID:SCR_000121) Copy   

•   Source: SciCrunch Registry

https://simtk.org/home/aspf

Scalable particle fluid simulation code for Lagrangian particle-based fluid simulation. This adaptive sampling strategy allows using smaller (and thus more) particles in geometrically complex regions, while less particles are used for thick flat fluid volumes. Additionally, a novel distance-based particle surface definition is implemented which hides the particle granularity and allows dynamic resampling near the fluid-air interface. The code is implemented in C++ and should compile on Linux.

Proper citation: Adaptively Sampled Particle Fluids (RRID:SCR_000083) Copy   

•   Source: SciCrunch Registry

http://biolemmatizer.sourceforge.net/

A domain-specific lemmatization software tool for the morphological analysis of biomedical literature.

Proper citation: BioLemmatizer (RRID:SCR_000117) Copy   

•   Source: SciCrunch Registry

http://orphelia.gobics.de/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. A metagenomic open reading frame (ORF) finding tool for the prediction of protein coding genes in short, environmental DNA sequences with unknown phylogenetic origin. The resource is based on a two-stage machine learning approach that uses linear discriminants to extract features from the ORFs. An artificial neural network then combines the features and computes a gene probability for each ORF fragment.

Proper citation: Orphelia (RRID:SCR_000119) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ReQON.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.

Proper citation: ReQON (RRID:SCR_000075) Copy   

•   Source: SciCrunch Registry

http://www.iro.umontreal.ca/~csuros/quadgt/

Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.

Proper citation: QuadGT (RRID:SCR_000073) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/

A free online service to easily create and share webpages.

Proper citation: Google Sites (RRID:SCR_000112) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/soapfuse.html

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .

Proper citation: SOAPfuse (RRID:SCR_000078) Copy   

•   Source: SciCrunch Registry

http://www.genemed.com/

A supplier of cancer and infectious disease diagnostic reagents. The company also provides services such as tissue-based and molecular diagnostics to their partners to accelerate their in vitro diagnostic device (IVD) product development and commercialization.

Proper citation: Genemed (RRID:SCR_000070) Copy   

•   Source: SciCrunch Registry

http://www.cogsci.ucsd.edu/media/uploads/grad/grad_fellowship_info.pdf

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. This resource is a frequently updated listing of graduate student in cognitive science fellowship opportunities. For current opportunities, please see the PDF document.

Proper citation: University of California at San Diego Cognitive Science Graduate Student Fellowship Opportunities (RRID:SCR_000105) Copy   

•   Source: SciCrunch Registry