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http://sourceforge.net/projects/viralfusionseq/

A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required.

Proper citation: VFS (RRID:SCR_005138) Copy   

•   Source: SciCrunch Registry

https://github.com/tk2/RetroSeq

A tool for discovery and genotyping of transposable element variants (TEVs) (also known as mobile element insertions) from next-gen sequencing reads aligned to a reference genome in BAM format. The goal is to call TEVs that are not present in the reference genome but present in the sample that has been sequenced. It should be noted that RetroSeq can be used to locate any class of viral insertion in any species where whole-genome sequencing data with a suitable reference genome is available. RetroSeq is a two phase process, the first being the read pair discovery phase where discorandant mate pairs are detected and assigned to a TE class (Alu, SINE, LINE, etc.) by using either the annotated TE elements in the reference and/or aligned with Exonerate to the supplied library of viral sequences.

Proper citation: RetroSeq (RRID:SCR_005133) Copy   

•   Source: SciCrunch Registry

https://github.com/cwhelan/cloudbreak

Software providing a Hadoop-based genomic structural variation (SV) caller for Illumina paired-end DNA sequencing data. It contains a full pipeline for aligning data in the form of FASTQ files using alignment pipelines that generate many possible mappings for every read, in the Hadoop framework. It then contains Hadoop jobs for computing genomic features from the alignments, and for calling insertion and deletion variants from those features.

Proper citation: Cloudbreak (RRID:SCR_005097) Copy   

•   Source: SciCrunch Registry

http://mcb.berkeley.edu/labs/werblin/index.html

The goal of our research is to uncover the neural circuitry that mediates some of the remarkable processing capabilities of the retina. The retina to operates at high spatial and temporal resolution over more than 7 orders of magnitude, to detect the direction of motion, to blank and then recover after saccades, to generate at least a dozen different abstract representations of the visual world. How is all of this, and much more, possible in this tissuepaper-thin array of neurons? Videos and images describing this include: * The retinal hypercircuit. * How the Retina Works * Take a Tour through the Retina * Cartoon of the retina showing layering of neurons * Directional Selectivity * Feedback and Crossover inhibition * Multiple Representations of the Visual Scene ** Pseudo Array Recording Methods ** Multiple Representations of the Visual World ** Regions of Frequency Space * Regions of space/time frequency * Space-time rasters for ON and OFF cells * Patching a neuron in a retinal slice * Targeting Retinal Neuron Subregions with Arficial Rhodopsins

Proper citation: Werblin Lab (RRID:SCR_005251) Copy   

•   Source: SciCrunch Registry

http://www.slu.edu/x23032.xml

A brain bank which provides brain tissue for interdisciplinary research in neurochemical, anatomical, epidemiological and clinical aspects of Alzheimer's disease. It provides brain tissue from Alzheimer's patients and healthy elderly brain donors to investigators who are helping further the understanding of Alzheimer's disease through research. It also gives family members of Alzheimer's patients the opportunity to obtain a confirmed diagnosis through brain autopsy. Through this program, families of individuals with either a clinical diagnosis, or those with suspected Alzheimer's disease, grant permission for a brain autopsy to be performed immediately after death.

Proper citation: St. Louis University Alzheimer's Brain Bank (RRID:SCR_005132) Copy   

•   Source: SciCrunch Registry

http://www.genmapp.org/

GenMAPP is a free computer application designed to visualize gene expression and other genomic data on maps representing biological pathways and groupings of genes. Integrated with GenMAPP are programs to perform a global analysis of gene expression or genomic data in the context of hundreds of pathway MAPPs and thousands of Gene Ontology Terms (MAPPFinder), import lists of genes/proteins to build new MAPPs (MAPPBuilder), and export archives of MAPPs and expression/genomic data to the web. The main features underlying GenMAPP are: *Draw pathways with easy to use graphics tools *Color genes on MAPP files based on user-imported genomic data *Query data against MAPPs and the GeneOntology Enhanced features include the simultaneous view of multiple color sets, expanded species-specific gene databases and custom database options.

Proper citation: Gene Map Annotator and Pathway Profiler (RRID:SCR_005094) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/GRO-CPD

A structured controlled vocabulary for describing cereal plant development and growth stages. Please note that this ontology has now been superseded by the Plant Ontology.

Proper citation: Cereal Plant Development Ontology (RRID:SCR_005095) Copy   

•   Source: SciCrunch Registry

http://www.alzheimersinfo.org/index.html

A national research center that conducts research for Alzheimer's disease, stroke and other nervous system disorders. The mission of the Center is to improve the treatment and prevention of Alzheimer's disease and other neurologic disorders by advancing scientific knowledge through creative and collaborative research.

Proper citation: Regions Hospital Alzheimer's Research Center (RRID:SCR_005128) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/phenoman/

An interactive software program that integrates phenotypic data exploration, selection, management and quality control using a unified platform for association studies of rare and common variants.

Proper citation: PhenoMan (RRID:SCR_005249) Copy   

•   Source: SciCrunch Registry

http://www.murdock-trust.org/

The M. J. Murdock Charitable Trust seeks to enrich the quality of life in the Pacific Northwest by providing grants and enrichment programs to non-profit organizations that seek to strengthen the region''s educational, spiritual, and cultural base in creative and sustainable ways. In addition to a special interest in education and scientific research, the Trust partners with a wide variety of organizations that serve the arts, public affairs, health and medicine, human services, leadership development, and persons with disabilities. Eligibility for scientific research grants is limited. Select public research universities and medical institutes located within the five-state region (Pacific Northwest: Alaska, Washington, Oregon, Idaho, Montana) are typically considered for funding. The Trust prefers requests for projects in the natural sciences where the main objective is the acquisition of new knowledge. However, requests for research in engineering and medicine are also eligible. Training students in conducting research is an important consideration.

Proper citation: MJ Murdock Charitable Trust (RRID:SCR_005122) Copy   

•   Source: SciCrunch Registry

http://www.nasonline.org/news-and-multimedia/podcasts/

Subscribe to the National Academy of Sciences podcasts to learn more about scientists and their work, the latest in research, and key findings of National Research Council reports. * InterViews: InterViews provides first-person accounts of the lives and work of National Academy of Sciences members. In this series of one-on-one conversations, scientists talk about what inspired them to pursue the careers they chose and describe some of the most fascinating aspects of their research. * Science Sessions: The Proceedings of the National Academy of Sciences offers brief, 5-minute, nontechnical conversations with cutting-edge researchers, including members of the National Academy of Sciences, and policymakers as they discuss topics relevant to today''s scientific community. Learn the behind-the-scenes story of work published in PNAS, plus a broad range of scientific news about discoveries that affect the world around us. * News from the National Academies: Listen to the latest news conferences and public briefings on National Research Council and Institute of Medicine reports. * Sounds of Science: This informative and entertaining series puts a spotlight on the high-impact work of the National Research Council. Focusing on a wide range of critical issues in science, engineering, and medicine, these short episodes are a quick and easy way to tune in our key findings and important recommendations. * Cultural Programs: The Cultural Programs of the National Academy of Sciences presents public exhibitions, lectures, and other programs exploring the intersections of art, science, and culture. The podcast features audio recordings of past lectures and other events. * Engineering Innovation: This weekly podcast from the National Academy of Engineering highlights exciting developments in engineering and provides technical context to stories in the news. The 40-second episodes demonstrate how engineers are making an impactin energy, health, the environment, sports, and more.

Proper citation: National Academy of Sciences Podcasts (RRID:SCR_005124) Copy   

•   Source: SciCrunch Registry

http://www.calacademy.org/teachers/families/

Family Science - Fun activities to do at home, on the web, in the Academy and more. The program serves San Francisco''s fourth and fifth grade teachers, students and their families. The Rock Program We are excited to welcome you, your students and their families to the Enhanced Museum Visits for Students Program. Generously funded by Arthur and Toni Rembe Rock, this program is open to all 4th and 5th grade classes within San Francisco County lines. Each of the following FREE features are built into the field trip program to support and enrich the museum experience for teachers, students and families: * Bus transportation - if needed * Teacher workshops that highlight exhibit themes and educational resources (required for first time participants, optional for repeat teachers) * Educational programs designed to enhance the museum visit fieldtrip for your students * A student pass entitling each student unlimited free admission through August * A one-time free family pass with a science activity book for each student valid through the end of August.

Proper citation: California Academy of Sciences Family Science (RRID:SCR_005241) Copy   

•   Source: SciCrunch Registry

http://www.omicsoft.com/fusionmap/

An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies. FusionMap runs under both Windows and Linux (requiring MONO) environments. Although it can run on 32 bit machine, it is recommended to run on 64-bit machine with 8GB RAM or more. If you have an ArrayStudio License, you can run the fusion detection easily through its GUI.

Proper citation: FusionMap (RRID:SCR_005242) Copy   

•   Source: SciCrunch Registry

http://www.cs.helsinki.fi/en/gsa/traph/

A software tool for transcript identification and quantification with RNA-Seq. The method has a two-fold advantage: on the one hand, it translates the problem as an established one in the field of network flows, which can be solved in polynomial time, with different existing solvers; on the other hand, it is general enough to encompass many of the previous proposals under the least sum of squares model.

Proper citation: Traph (RRID:SCR_005119) Copy   

•   Source: SciCrunch Registry

http://jobs.newscientist.com/

At New Scientist Jobs you can search our database for hundreds of Science and Technology jobs from across the globe. Registration is free and you can upload your resume, set up email job alerts, subscribe to RSS feeds and apply for Science and Technology jobs online. Employers can post jobs. We also work in partnership with the science and academic community to help them recruit the right Science and Technology candidates for their vacancies online.

Proper citation: New Scientist Jobs (RRID:SCR_005155) Copy   

•   Source: SciCrunch Registry

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