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http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html

Software which performs accurate and fast mapping of bisulfite-treated short reads. Supplementary information and examples are provided on the site.

Proper citation: BS Seeker (RRID:SCR_005641) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/about/advisory-boards-and-groups/namhc/reports/mri-research-safety-ethics.pdf

NIMH recognizes the need to consider safety and ethical issues related to both the administration of MR (magnetic resonance) facilities and the use of these facilities for research. This document summarizes the points to consider discussed by the National Advisory Mental Health Council (NAMHC) Workgroup. Examples of safe and ethical practices are discussed in relation to several issues. These examples are intended to be illustrative and should not be interpreted as an exhaustive or exclusive list. This document was presented to the full NIMH Council on September 15, 2006 and approved unanimously. By making the points to consider document available publicly, NIMH intends to provide a resource for researchers and institutions that use MRI in research. The agenda was organized into six topics, which provide the organization for the points to consider that follow: A. MRI screening B. Training, operating, and emergency procedures C. Physical facilities D. Scanning/participant health variables E. Context- Specific Considerations: University vs. medical settings F. Additional data needs and updating The NIMH believes that investigators, institutions and facilities can use this document as a resource for the development, administration, evaluation, and use of MRI research facilities.

Proper citation: MRI Research Safety and Ethics (RRID:SCR_005642) Copy   

•   Source: SciCrunch Registry

http://fcon_1000.projects.nitrc.org/

Collection of resting state fMRI (R-fMRI) datasets from sites around world. It demonstrates open sharing of R-fMRI data and aims to emphasize aggregation and sharing of well-phenotyped datasets.

Proper citation: 1000 Functional Connectomes Project (RRID:SCR_005361) Copy   

•   Source: SciCrunch Registry

http://www.cma.mgh.harvard.edu/iatr/

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. It is hoped that this helps the tool developers to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development. This also helps tool users in identification of the existing tools for specific problems as they arise. The registry is designed to be self-moderated. This means that all tool entries are owned by some responsible party who enters the tool information, and keeps it up to date via the Web.

Proper citation: Internet Analysis Tools Registry (RRID:SCR_005638) Copy   

•   Source: SciCrunch Registry

http://ocw.mit.edu/index.htm

A web-based publication of virtually all MIT course content for free. OCW is open and available to the world and is a permanent MIT activity. Materials include free lecture notes, exams, and videos from MIT. No registration required. MIT OpenCourseWare is a free publication of MIT course materials that reflects almost all the undergraduate and graduate subjects taught at MIT. * OCW is not an MIT education. * OCW does not grant degrees or certificates. * OCW does not provide access to MIT faculty. * Materials may not reflect entire content of the course. A site overview is available for MIT OpenCourseWare. You can also browse courses by department or use the advanced search to locate a specific course or topic. High school students and educators should check out Highlights for High School.

Proper citation: MIT OpenCourseWare (RRID:SCR_005555) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/rseqc/

Software package to comprehensively evaluate different aspects of RNA-seq experiments, such as sequence quality, GC bias, polymerase chain reaction bias, nucleotide composition bias, sequencing depth, strand specificity, coverage uniformity and read distribution over the genome structure. RSeQC takes both SAM and BAM files as input, which can be produced by most RNA-seq mapping tools as well as BED files, which are widely used for gene models.

Proper citation: RSeQC (RRID:SCR_005275) Copy   

•   Source: SciCrunch Registry

http://www.med.harvard.edu/AANLIB/

An atlas of normal and abnormal brain images intended as an introduction to basic neuroanatomy, with emphasis on the pathoanatomy of several leading central nervous system diseases that integrates clinical information with magnetic resonance (MR), x-ray computed tomography (CT), and nuclear medicine images. A range of brain abnormalities are presented including examples of certain brain disease presented with various combinations of image type and imaging frequency. Submissions of concise, exemplary, clinically driven examples of neuroimaging are welcome.

Proper citation: Whole Brain Atlas (RRID:SCR_005390) Copy   

•   Source: SciCrunch Registry

http://llama.mshri.on.ca/synergizer/translate/

The Synergizer database is a growing repository of gene and protein identifier synonym relationships. This tool facilitates the conversion of identifiers from one naming scheme (a.k.a namespace) to another. The Synergizer is a service for translating between sets of biological identifiers. It can, for example, translate Ensembl Gene IDs to Entrez Gene IDs, or IPI IDs to HGNC gene symbols, and much more. Unlike some other tools for this purpose, The Synergizer is simple and easy to learn. The Synergizer works via a web interface (for users who are not programmers) or through a web service (for programmatic access).

Proper citation: Synergizer (RRID:SCR_005308) Copy   

•   Source: SciCrunch Registry

http://geneontology.svn.sourceforge.net/viewvc/geneontology/go-moose/

go-moose is intended as a replacement for the aging go-perl and go-db-perl Perl libraries. It is written using the object oriented Moose libraries. It can be used for performing a number of analyses on GO data, including the remapping of GO annotations to a selected subset of GO terms. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: go-moose (RRID:SCR_005666) Copy   

•   Source: SciCrunch Registry

http://hmmer.janelia.org/

Tool for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.

Proper citation: Hmmer (RRID:SCR_005305) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.mdanderson.org/main/SpliceSeq:Overview

A Java application to investigate alternative mRNA splicing patterns in data from high-throughput mRNA sequencing studies. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing. This tool may be used on a single RNASeq sample to identify genes with multiple spliceforms, on a pair of samples to identify differential splicing between the two, or on groups of samples to identify statistically significant group level differences in splicing patterns. SpliceSeq can be run from the install page as a java web start application to explore the sequencing data on their server or can be installed locally to analyze your own mRNA-Seq data.

Proper citation: SpliceSeq (RRID:SCR_005267) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/scicrunch/data/source/nlx_154697-14/search?q=*

A virtual database currently indexing the following scientific Job resources: Naturejobs, Monster, Indeed, Hays, jobs.ac.uk, New Scientist Jobs, Science Careers, Access-ScienceJobs.co.uk, TheScienceJobs.com, ScienceBlogs: Jobs, and It Takes 30.

Proper citation: Integrated Jobs (RRID:SCR_005384) Copy   

•   Source: SciCrunch Registry

http://ontogenesis.knowledgeblog.org/

Knowledge Blog for descriptive, tutorial and explanatory material about building, using and maintaining ontologies, as well as the social processes and technology that support this. Ontogenesis features over 20 articles written by leading academics, and has attracted over 17,000 page reads. Articles are peer-reviewed. Following publication as reviewed, articles are stable and can be cited by stable URL or DOI. Ontogenesis is now archived by the British Library as part of the UK Web Archive and is indexed by Google Scholar. The initial idea for Ontogenesis came from Phillip Lord. You can read the original manifesto that they wrote, describing the purpose of this blog. Ontogenesis is the first and main example of a Knowledgeblog, a flexible and light-weight process for scientific publication. It has received funding from JISC. They are currently open to submissions. Please contact them if you want further information, or would like to offer articles for publication., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Ontogenesis (RRID:SCR_005380) Copy   

•   Source: SciCrunch Registry

http://taverna.knowledgeblog.org/

Taverna Knowledge Blog: Designing, Executing and Sharing Scientific workflows

Proper citation: Taverna Knowledge Blog (RRID:SCR_005381) Copy   

•   Source: SciCrunch Registry

http://cvcweb.ices.utexas.edu/cvcwp/?page_id=100

VolumeRover (a.k.a VolRover) is an interactive multi-purpose image processing software that can visualize three dimensional imaging data of any size (as big as terabyte) in a commodity PC or workstation and additionally supports the following image processing operations. Image Contrast Enhancement, Filtering/Noise Reduction, Image Segmentation, Isocontouring, Symmetry Detection (for Virus Maps, Boundary-free Image Skeletonization. VolRover provides a user interface to a number of CVC software packages including Segmentation, Contrast Enhancement, and Motif Elucidation.

Proper citation: VolumeRover (RRID:SCR_005457) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ua.pt/becas/

Web application, API and widget able to recognize and annotate biomedical concepts in text.Provides annotations for isolated, nested and intersected entities.Identifies concepts from multiple semantic groups, providing preferred names and enriching them with references to public knowledge resources.

Proper citation: becas (RRID:SCR_005337) Copy   

•   Source: SciCrunch Registry

http://www.bscs.org/science-mental-illness

A set of lessons for students used to gain insight into the biological basis of mental illnesses and how scientific evidence and research can help us understand its causes and lead to treatments and, ultimately, cures. Both the Web version and the free supplement are available. It is a creative, inquiry-based instruction program designed to promote active learning and stimulate student interest in medical topics. This curriculum supplement aims to help students experience the process of scientific inquiry and develop an enhanced understanding of the nature and methods of science.

Proper citation: Science of Mental Illness: Grades 6- 8 (RRID:SCR_005612) Copy   

•   Source: SciCrunch Registry

http://www.genexplain.com/

An online toolbox and workflow management system for a broad range of bioinformatic and systems biology applications. The individual modules, or Bricks, are unified under a standardized interface, with a consistent look-and-feel and can flexibly be put together to comprehensive workflows. The workflow management is intuitively handled through a simple drag-and-drop system. With this system, you can edit the predefined workflows or compose your own workflows from scratch. Your own Bricks can easily be added as scripts or plug-ins and can be used in combination with pre-existing analyses. GeneXplain GmbH provides a number of state-of-the-art bricks; some of them can be obtained free of charge, while others require licensing for small fee in order to guarantee active maintenance and dynamic adaptation to the rapidly developing know-how in this field.

Proper citation: geneXplain (RRID:SCR_005573) Copy   

•   Source: SciCrunch Registry

http://bioinfo.unice.fr/

Virtual Biology Lab portal from the University of Nice Sophia Antipolis; Nice; France. Offered are a variety of software including: * GenBank2Treedyn: Extract annotations from GenBank files for: ** More convenient alignments and phylogeny (replace def line of fasta file by GI number) ** Extremely powerful annotations of phylogenetic trees with TreeDyn. * THEA: Analyses of DNA chip data with ontologies * Blast2Tree: Blast server for the identification of procaryotes * Dashboard: e-Tool for data exchanges among partners, DNA chips design and developement * Oligo Heat Map: Check thermodynamical parameters for PCR primers and compute graphical representation to show specificity of target sequences * EmblEx: A cgi tool to parse and extract data from EMBL entries to various formats * Miscellaneous software ** Jane plugin: Add a small panel to Jane server to retrieve PMID of publications ** EtBlast plugin: Add a small panel to EtBlast server to retrieve PMID of publications ** Oligo Builder: Get the oligomers from a set of target sequences by avoiding non-target sequences

Proper citation: Virtual Biology Lab (RRID:SCR_005694) Copy   

•   Source: SciCrunch Registry

https://biit.cs.ut.ee/

The Bioinformatics, Algorithmics, and Data Mining group BIIT lead by prof. Jaak Vilo is a joint research group between the Department of Computer Science (University of Tartu), Quretec, and the Estonian Biocenter. Our main research topics and capabilities include the gene regulation, gene expression data analysis, biological data mining, systems biology, combinatorial pattern matching, developing software for biomedical research databases, as well as partnering in stem cell and cancer related projects. Software * MEM - Multi-Experiment-Matrix -- large-scale gene expression data queries and mining (Genome Biology 2009) * g:Profiler family of tools for functional assessment of gene groups, gene ID mappings, orthology and expression similarity searches. (NAR web server issue 2007) * KEGGanim - visualisation of high-throughput data on biological pathway charts (Bioinformatics, 2007) * GraphWeb - a tool for mining large biological networks (NAR Web server issue 2008) * FunGenES data atlas * More software tools

Proper citation: BIIT - Bioinformatics Algorithmics and Data Mining Group (RRID:SCR_005690) Copy   

•   Source: SciCrunch Registry