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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   

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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   

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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   

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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   

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http://taverna.knowledgeblog.org/

Taverna Knowledge Blog: Designing, Executing and Sharing Scientific workflows

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

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http://www.aids.org/

The mission of AIDS.ORG is to help prevent HIV infections and to improve the lives of those affected by HIV and AIDS by providing education and facilitating the free and open exchange of knowledge at an easy-to-find centralized website. AIDS.ORG makes access to important AIDS information easier and faster. We provide prevention, testing, and treatment information currently to well over 4 million people a year. AIDS.ORG has been awarded the Health on the Net Foundation Code of Conduct (HONcode) seal for reliability and credibility of information in the field of healthcare. Additionally, every year over 2.4 million young people under the age of 25 turn to AIDS.ORG, making us an important resource since over 50% of all new HIV infections in the USA occur in this age group. AIDS.ORG, Inc. is a nonprofit 501(c) (3) educational organization, and maintains a very strict privacy policy. We make it our goal to be the best starting point for someone looking for AIDS information on the Internet. Our intent is that users be directed to the best information on the topic they''re investigating. We bring people together to share knowledge and experiences. In the past, we also provided the very first Internet-based program of accredited AIDS education for medical professionals, allowing doctors in rural and isolated areas to better serve AIDS patients.

Proper citation: AIDS.org (RRID:SCR_005537) 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   

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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://science.kqed.org/quest/

An award-winning multimedia science and environment series created by KQED, San Francisco, the public media station serving Northern California. Launched in February 2007, by the end of its fourth season (in September 2010), QUEST had reached approximately 36 million viewers and listeners through its traditional TV and radio broadcasts and its growing Web audience. QUEST''s ultimate aim is to raise science literacy in the San Francisco Bay Area and beyond, inspiring audiences to discover and explore science and environment issues for themselves. Every season, KQED''s QUEST produces: * half-hour television episodes episodes that air weekly, exploring the cutting-edge work of Northern California scientists and researchers (QUEST airs Wednesdays 7:30pm on KQED Public Television 9); * weekly radio reports covering urban environmental issues which often include multimedia slide shows, and interactive online maps (QUEST airs Mondays 6:30am and 8:30am on KQED Public Radio 88.5 FM); * Educational resources, for use by formal and informal educators; QUEST also provides professional development for science educators to support multimedia and technology integration in science classrooms and programs; * 20 six-minute stories for its new web only series, Science on the SPOT, which takes a fresh, fast and curious look at science with stories about albino redwoods, the science of fog and banana slugs, to name a few. (launched in 2010); * A daily science blog written by Northern California scientists, QUEST producers and science enthusiasts; * Exclusive web extras, featuring extended interviews with scientists; Flickr photos, and science hikes. Formal and informal Educators who would like to become involved withthe educational outreach program should contact: ScienceEd (at) kqed.org.

Proper citation: QUEST (RRID:SCR_005210) Copy   

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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://science.education.nih.gov/home2.nsf/feature/index.htm

The NIH Office of Science Education (OSE) coordinates science education activities at the NIH and develops and sponsors science education projects in house. These programs serve elementary, secondary, and college students and teachers and the public. Activities * Develop curriculum supplements and other educational materials related to medicine and research through collaborations with scientific experts at NIH * Maintain a website as a central source of information about NIH science education resources * Establish national model programs in public science education, such as the NIH Mini-Med School and Science in the Cinema * Promote science education reform as outlined in the National Science Education Standards and related guidelines The OSE was established in 1991 within the Office of Science Policy of the Office of the Director of the National Institutes of Health. The NIH is the world''s foremost biomedical research center and the U.S. federal government''s focal point for such research. It is one of the components of the Department of Health and Human Services (HHS). The Office of Science Education (OSE) plans, develops, and coordinates a comprehensive science education program to strengthen and enhance efforts of the NIH to attract young people to biomedical and behavioral science careers and to improve science literacy in both adults and children. The function of the Office is as follows: (1) develops, supports, and directs new program initiatives at all levels with special emphasis on targeting students in grades kindergarten to 16, their educators and parents, and the general public; (2) advises NIH leadership on science education issues; (3) examines and evaluates research and emerging trends in science education and literacy for policy making; (4) works closely with the NIH extramural, intramural, women''s health, laboratory animal research, and minority program offices on science education special issues and programs to ensure coordination of NIH efforts; (5) works with NIH institutes, centers, and divisions to enhance communication of science education activities; and (6) works cooperatively with other public- and private-sector organizations to develop and coordinate activities.

Proper citation: NIH Office of Science Education (RRID:SCR_005603) Copy   

•   Source: SciCrunch Registry

http://bioportal.bioontology.org/annotator

A Web service that annotates textual metadata (e.g. journal abstract) with relevant ontology concepts. NCBO uses this Web service to annotate resources in the NCBO Resource Index. They also provide this Web service as a stand-alone service for users. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Their service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards.

Proper citation: NCBO Annotator (RRID:SCR_005329) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/educational-resources/brain-basics/brain-basics.shtml

Brain Basics provides information on how the brain works, how mental illnesses are disorders of the brain, and ongoing research that helps us better understand and treat disorders. Mental disorders are common. You may have a friend, colleague, or relative with a mental disorder, or perhaps you have experienced one yourself at some point. Such disorders include depression, anxiety disorders, bipolar disorder, attention deficit hyperactivity disorder (ADHD), and many others. Some people who develop a mental illness may recover completely; others may have repeated episodes of illness with relatively stable periods in between. Still others live with symptoms of mental illness every day. They can be moderate, or serious and cause severe disability. Through research, we know that mental disorders are brain disorders. Evidence shows that they can be related to changes in the anatomy, physiology, and chemistry of the nervous system. When the brain cannot effectively coordinate the billions of cells in the body, the results can affect many aspects of life. Scientists are continually learning more about how the brain grows and works in healthy people, and how normal brain development and function can go awry, leading to mental illnesses. Brain Basics will introduce you to some of this science, such as: * How the brain develops * How genes and the environment affect the brain * The basic structure of the brain * How different parts of the brain communicate and work with each other * How changes in the brain can lead to mental disorders, such as depression.

Proper citation: Brain Basics (RRID:SCR_005606) Copy   

•   Source: SciCrunch Registry

http://services.nbic.nl/copub/portal/

Text mining tool that detects co-occuring biomedical concepts in abstracts from the MedLine literature database. It allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs.

Proper citation: CoPub (RRID:SCR_005327) Copy   

•   Source: SciCrunch Registry

http://202.97.205.78/CpG_MPs/

Tool for identification and analysis of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. It may identify the unmethylated and methylated regions for a single sample, the conserved and differential methylation regions with different methylation patterns for paired or multiple samples. It includes four main modules as follows: # Normalization of the sequencing reads of cytosines following guanines; # Identification of the unmethylated (methylated) regions using hotspot extension algorithm; # Identification of conservatively and differentially methylated regionsby combining the combinatorial algorithm for determination of potentially functional regions with the algorithm of analysis of variance (ANOVA) for assess the statistical significance of differentially methylated regions; # Extraction of sequence features and visualization of these potentially functional regions.

Proper citation: CpG MPs (RRID:SCR_005441) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CABRO

A web ontology for the semantic representation of the computer assisted brain trauma rehabilitation domain. This is a novel and emerging domain, since it employs the use of robotic devices, adaptation software and machine learning to facilitate interactive, adaptive and personalized rehabilitation care, patient monitoring and assisted living.

Proper citation: Computer Assisted Brain Injury Rehabilitation Ontology (RRID:SCR_005288) Copy   

•   Source: SciCrunch Registry

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

Central location for voluntary submission of genetic test information by providers including the test''s purpose, methodology, validity, evidence of the test''s usefulness, and laboratory contacts and credentials. GTR aims to advance the public health and research into the genetic basis of health and disease. GTR is accepting registration of clinical tests for Mendelian disorders, complex tests and arrays, and pharmacogenetic tests. These tests may include multiple methods and may include multiple major method categories such as biochemical, cytogenetic, and molecular tests. GTR is not currently accepting registration of tests for somatic disorders, research tests or direct-to-consumer tests.

Proper citation: Genetic Testing Registry (RRID:SCR_005565) Copy   

•   Source: SciCrunch Registry

http://www.biological-networks.org/pubs/suppl/sinomo/

Analysis-tool which identifies singular node motifs in a network. Network nodes can be described by node-motifs. It is an improvement to the method described in Costa et al. (2009).

Proper citation: SINOMO (RRID:SCR_005286) Copy   

•   Source: SciCrunch Registry

http://en.wikibooks.org/wiki/MINC/Atlases

A linear average model atlas produced by the International Consortium for Brain Mapping (ICBM) project. A set of full- brain volumetric images from a normative population specifically for the purposes of generating a model were collected by the Montreal Neurological Institute (MNI), UCLA, and University of Texas Health Science Center at San Antonio Research Imaging Center (RIC). 152 new subjects were scanned using T1, T2 and PD sequences using a specific protocol. These images were acquired at a higher resolution than the original average 305 data and exhibit improved contrast due predominately to advances in imaging technology. Each individual was linearly registered to the average 305 and a new model was formed. In total, three models were created at the MNI, the ICBM152_T1, ICBM152_T2 and ICBM152_PD from 152 normal subjects. This resulting model is now known as the ICBM152 (although the model itself has not been published). One advantage of this model is that it exhibits better contrast and better definition of the top of the brain and the bottom of the cerebellum due to the increased coverage during acquisition. The entirely automatic analysis pipeline of this data also included grey/white matter segmentation via spatial priors. The averaged results of these segmentations formed the first MNI parametric maps of grey and white matter. The maps were never made publicly available in isolation but have formed parts of other packages for some time including SPM, FSL AIR and as models of grey matter for EEG source location in VARETTA and BRAINWAVE. Again, as these models are an approximation of Talairach space, there are differences in varying areas, to continue our use of origin shift as an example, the ICBM models are approximately 152: +3.5mm in Z and +-co-ordinate -3.5mm and 2.0mm in Y as compared to the original Talairach origin. In addition to the standard analysis performed on the ICBM data, 64 of the subjects data were segmented using model based segmentation. 64 of the original 305 were manually outlined and a resulting parametric VOI atlas built. The native data from these acquisitions was 256x256 with 1mm slices. The final image resolution of this data was 181x217x181 with 1mm isotropic voxels. Refer to the ICBM152 NonLinear if you are fitting an individual to model and do not care about left/right comparisons. A short history of the various atlases that have been produced at the BIC (McConnell Brain Imaging Center, Montreal Neurological Institute) is provided.

Proper citation: MINC/Atlases (RRID:SCR_005281) Copy   

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http://bioimage.ucsb.edu/bisque

Open source database for exchange and exploration of biological images. Used to store, visualize, organize and analyze images in cloud. Centered around database of images and metadata.

Proper citation: Bisque database (RRID:SCR_005559) Copy   

•   Source: SciCrunch Registry