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http://www.raetschlab.org/suppl/rquant

Software for quantitative detection of alternative transcripts with RNA-Seq data. The method, based on quadratic programming, estimates biases introduced by experimental settings and is thus a powerful tool to reveal and quantify novel (alternative) transcripts.

Proper citation: rQuant (RRID:SCR_005150) Copy   

•   Source: SciCrunch Registry

http://www.med.umkc.edu/psychiatry/nbtb/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The UMKC Neuroscience Brain Tissue Bank and Research Laboratory has been established to obtain, process, and distribute human brain tissue to qualified scientists and clinicians dedicated to neuroscience research. No other living organ approaches the human brain in complexity or capacity. Healthy, it astounds and inspires miracles. Diseased, it confounds and diminishes hope. The use of human brain tissue for research will provide insight into the anatomical and neurochemical aspects of diseased and non-diseased brains. While animal models are helpful and necessary in understanding disease, certain disorders can be more efficiently studied using human brain tissue. Also, modern research techniques are often best applied to human tissue. We also need samples of brain tissue that have not been affected by disease. They help us to compare a 'normal' brain with a diseased one. Also, we have a critical need for brain donations from relatives who have genetically inherited disorders. Tissue preparation consists of fresh quick-frozen tissue blocks or coronal slices (nitrogen vapor frozen; custom dissection of specific anatomic regions) or formalin-fixed coronal slices (custom dissection of specific anatomic regions).

Proper citation: UMKC Neuroscience Brain Tissue Bank and Research Laboratory (RRID:SCR_005148) Copy   

•   Source: SciCrunch Registry

http://www.rls.org/

Non-profit organization providing the latest information about Restless Legs Syndrome (RLS). Its goals are to increase awareness, improve treatments, and through research, find a cure for RLS, a condition which severely affects the lives of millions of individuals. By educating healthcare providers about RLS symptoms, diagnosis, and treatment, the RLS Foundation helps patients receive the quality care they both need and deserve. In recent years the Foundation has provided information to healthcare providers at many exhibit meetings, including the American Academy of Neurology, the American College of Obstetricians and Gynecologists, and the American Academy of Nurse Practitioners. The Foundation continually strives to be the most reputable source of information on RLS. Their renowned Medical Advisory Board, composed of leading RLS experts from all over the world, has written several publications on the diagnosis and treatment of RLS. These include our comprehensive RLS Medical Bulletin, their patient brochure, and their brochures on special topics including concerns for surgery, depression, pregnancy, and children. The Foundation has taken giant strides to further RLS research, funding grants for 27 research projects. Among the most distinguished research projects the Foundation has put its resources behind is the ongoing Stanford Epidemiology Project. Although it is still underway, the Foundation recognizes that the highly anticipated results of the Stanford Epidemiology Project, including the creation of a world standard questionnaire used to accurately diagnose RLS, could be spectacular. Eventually this questionnaire may help researchers understand the health consequences of RLS and identify other conditions and diseases that are associated with or exacerbated by RLS. In addition, the RLS Foundation helped fund a study led by Dr. David Rye and deCODE Genetics in Iceland which recently announced the discovery of a gene for RLS.

Proper citation: RLS Foundation (RRID:SCR_005144) Copy   

•   Source: SciCrunch Registry

https://knightadrc.wustl.edu/center-events/

Videos of Knight ADRC related events for educational and informational purposes. A link to additional Center produced media is provided to access the Knight ADRC YouTube Channel. Videos are in HTML5 mp4 format and are available in 1080p or 4K resolution.

Proper citation: WU Knight ADRC Multimedia Presentations (RRID:SCR_005147) Copy   

•   Source: SciCrunch Registry

http://www.uku.fi/english/

University of Eastern Finland was formed through merger of two formerly independent universities, the University of Joensuu and the University of Kuopio.Public University of Eastern Finland Kuopio Campus is located in the Savilahti area.

Proper citation: University of Eastern Finland at Kuopio; Kuopio; Finland (RRID:SCR_005214) 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   

•   Source: SciCrunch Registry

http://www.bsse.ethz.ch/cbg/software/shorah

A software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes.

Proper citation: ShoRAH (RRID:SCR_005211) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/v-phaser-2

A software tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. It combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. V-Phaser can reliably detect rare variants in diverse populations that occur at frequencies of <1%. V-Phaser 2 is a complete rewrite of the original V-Phaser. It contains a new model for length polymorphisms (indels) and incorporates paired end read information in its phasing model. The data access and probability computation sections of the code have also been highly optimized, resulting in substantial improvements in running time and memory usage.

Proper citation: V-Phaser 2 (RRID:SCR_005212) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/nsmapforrnaseq/

Software designed to identify and quantify isoforms from RNA-seq by incorporating a sparsity term into expression level estimation to enable isoform structure prediction and expression estimation simultaneously.

Proper citation: NSMAP (RRID:SCR_005213) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cova/

A variant annotation and comparison tool for next-generation sequencing. It annotates the effects of variants on genes and compares those among multiple samples, which helps to pinpoint causal variation(s) relating to phenotype.

Proper citation: COVA (RRID:SCR_005175) Copy   

•   Source: SciCrunch Registry

http://bmda.cs.unibas.ch/HivHaploTyper/

Software for reconstructing haplotypes from next-generation sequencing data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PredictHaplo (RRID:SCR_005207) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/qure/

A software program for viral quasispecies reconstruction, specifically developed to analyze long read (>100 bp) next-generation sequencing (NGS) data. The software performs alignments of sequence fragments against a reference genome, finds an optimal division of the genome into sliding windows based on coverage and diversity and attempts to reconstruct all the individual sequences of the viral quasispecies--along with their prevalence--using a heuristic algorithm, which matches multinomial distributions of distinct viral variants overlapping across the genome division. QuRe comes with a built-in Poisson error correction method and a post-reconstruction probabilistic clustering, both parameterized on given error rates in homopolymeric and non-homopolymeric regions.

Proper citation: QuRe (RRID:SCR_005209) Copy   

•   Source: SciCrunch Registry

http://bioinfo.mc.vanderbilt.edu/VirusFinder/

Software tool for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. Specifically, it detects virus infection, co-infection with multiple viruses, virus integration sites in host genomes, as well as mutations in the virus genomes. It also facilitates virus discovery by reporting novel contigs, long sequences assembled from short reads that map neither to the host genome nor to the genomes of known viruses. VirusFinder 2 works with both paired-end and single-end data, unlike the previous 1.x versions that accepted only paired-end reads. The types of NGS data that VirusFinder 2 can deal with include whole genome sequencing (WGS), whole transcriptome sequencing (RNA-Seq), targeted sequencing data such as whole exome sequencing (WES) and ultra-deep amplicon sequencing.

Proper citation: VirusFinder (RRID:SCR_005205) Copy   

•   Source: SciCrunch Registry

http://rnaexpress.org/

Software designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data.

Proper citation: RNA-eXpress (RRID:SCR_005167) Copy   

•   Source: SciCrunch Registry

http://scienceblogs.com/channel/jobs/?utm_source=globalChannel&utm_medium=link

ScienceBlogs posts about Jobs.

Proper citation: ScienceBlogs: Jobs (RRID:SCR_005200) Copy   

•   Source: SciCrunch Registry

http://tbgri.in/

Tropical Botanic Garden & Research Institute (TBGRI) is an autonomous Institute established by the Government of Kerala on 17th November 1979 and registered on 23rd November 1979 under the Travancore-Cochin Literary, Scientific and Charitable Societies Registration Act, 1955. It functions under the umbrella of the Science, Technology and Environment Department, Government of Kerala. Prof. A. Abraham, a visionary and a great Botanist, conceived the idea of establishing a Botanic Garden and Research Institute to study and conserve the rare and vanishing wild plant genetic resources of the country. Kinded by the spirit of his concept, the Government of Kerala took a far sighted decision resulting in the establishment of Tropical Botanic Garden & Research Institute (TBGRI) as an autonomous organization at Thiruvananthapuram, the capital City of Kerala. In the beginning, the Institute functioned at Thiruvananthapuram city on a rented duplex building. Thanks to the Forests & Wildlife Department, the land for establishment of the garden was allotted in 1983 and the foundation stone was laid on 27th May 1983 by the then Chief Minister, Shri K. Karunakaran. The then Education Minister, the late C. H. Mohammed Koya laid the foundation stone for the construction of the Visiting Scientists'' Guest House. The meeting was presided over by the Minister for Forests, Shri K. P. Noorudeen. With the recruitment of a skeletal scientific and technical staff, the Institute made a modest beginning. Biotechnology and Taxonomy were the two subjects considered to have immediate relevance to the development of the garden. While taxonomists prepared a flora of the garden documenting the native plant wealth before mass introduction and face lift which subsequently followed, the bio-technologists mass multiplied plants of commercial importance, especially orchids for cultivation and distribution to the public. The Royal Botanic Gardens (RBG), Kew played an exemplary and significant role in shaping and design of garden lay out of TBGRI in its formative stages. RBG, Kew not only lent its best men to train our technical staff in gardening and landscaping but also generously supplied books and living plants as gifts to enrich the respective collections. Undoubtedly, the continuing support of RBG, Kew is of special mention in the development of the Garden.

Proper citation: Tropical Botanic Garden and Research Institute (RRID:SCR_005162) Copy   

•   Source: SciCrunch Registry

http://unoseq.sourceforge.net/

A Java library to analyze next generation sequencing data and especially perform expression profiling in organisms where no well-annotated reference genome exists.

Proper citation: UnoSeq (RRID:SCR_005116) Copy   

•   Source: SciCrunch Registry

http://polygenic.jobamatic.com/a/jobs/find-jobs

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Featured Job Postings from the Web. Polygenic Pathways Jobs Job Site includes the latest jobs from polygenic.jobamatic.com. Post a job - only $5 for 100 days.

Proper citation: Polygenic Pathways Jobs (RRID:SCR_005237) Copy   

•   Source: SciCrunch Registry

http://gds.nih.gov/

NIH established expectations for sharing data obtained through NIH-funded genome-wide association studies (GWAS) with the implementation of the GWAS Policy. Information and resources related to the GWAS Policy can be found on this website.

Proper citation: Genomic Datasharing (RRID:SCR_005233) Copy   

•   Source: SciCrunch Registry

http://www.kavlifoundation.org/

The Kavli Foundation, based in Oxnard, California, is dedicated to advancing science for the benefit of humanity, promoting public understanding of scientific research, and supporting scientists and their work. The Foundation''s mission is implemented through an international program of research institutes, professorships, symposia and other initiatives in the fields of astrophysics, nanoscience, neuroscience and theoretical physics. The Foundation is also a founding partner of the Kavli Prizes, which recognize scientists for their seminal advances in astrophysics, nanoscience and neuroscience. To date, The Kavli Foundation has made grants to establish Kavli Institutes on the campuses of the University of California Santa Barbara, Stanford University, the California Institute of Technology, the University of Chicago, Columbia University, Yale University, Cornell University, the University of California San Diego, Delft University of Technology in the Netherlands, the Massachusetts Institute of Technology, Peking University, the Chinese Academy of Sciences, Harvard University, the University of Cambridge and the Norwegian University of Science and Technology. In addition to the Kavli Institutes, six Kavli professorships have been established: two at the University of California Santa Barbara, one at University of California Los Angeles, one at the University of California Irvine, one at Columbia University, and one at the California Institute of Technology. The Kavli Futures Symposia a series of high quality scientific symposia on topics of emerging importance in the fields of astrophysics, nanoscience and neuroscience. The Frontiers of Science symposia bring together some of the very best young scientists across many disciplines to share and discuss exciting advances and opportunities in their fields. Videos and feature pieces have been created for teachers and students. This includes video interviews with acclaimed researchers Eric Kandel, M.D. and Edvard and May-Britt Moser, a video introduction and panel discussion on neuroscience, feature stories, written science overview, institute profiles and other materials. The Kavli Foundation is a private foundation qualified under IRC Section 501 (c) (3).

Proper citation: Kavli Foundation (RRID:SCR_005113) Copy   

•   Source: SciCrunch Registry