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http://researchblogging.org/blog/home/id/882

A neuroscience blog written by Noah Gray.

Proper citation: Nothing's Shocking (RRID:SCR_000932) Copy   

•   Source: SciCrunch Registry

http://www.zfishbook.org/NGP/journalcontent/SCORE/SCORE.html

Narrative resource describing a visual data analysis and collection approach that takes advantage of the cylindrical nature of the zebrafish allowing for an efficient and effective method for image capture called, Specimen in a Corrected Optical Rotational Enclosure (SCORE) Imaging. To achieve a non-distorted image, zebrafish were placed in a fluorinated ethylene propylene (FEP) tube with a surrounding, optically corrected imaging solution: water. By similarly matching the refractive index of the housing (FEP tubing) to that of the inner liquid and outer liquid (water), distortion was markedly reduced, producing a crisp imagable specimen that is able to be fully rotated 360 degrees. A similar procedure was established for fixed zebrafish embryos using convenient, readily available borosilicate capillaries surrounded by 75% glycerol. The method described could be applied to chemical genetic screening and other, related high-throughput methods within the fish community and among other scientific fields.

Proper citation: Zebrafish - SCORE Imaging: Specimen in a Corrected Optical Rotational Enclosure (RRID:SCR_001300) Copy   

•   Source: SciCrunch Registry

http://collaborations.gis.a-star.edu.sg/~cmb6/TherMos/

Software used for estimating protein-DNA binding energies from in vivo binding profiles. It is a de novo motif discovery algorithm that exploits the information in transcription factor ChIP-seq or ChIP-exo datasets based on a more natural thermodynamic formalism., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TherMos (RRID:SCR_002790) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/enviPick/

Software for sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot.

Proper citation: enviPick (RRID:SCR_003059) Copy   

•   Source: SciCrunch Registry

http://www.incf.org/newsroom

Find all news and updates about INCF and neuroinformatics in the International Neuroinformatics Coordinating Facility (INCF) Newsroom.

Proper citation: INCF Newsroom (RRID:SCR_006493) Copy   

•   Source: SciCrunch Registry

http://mouse.cs.ucla.edu/emma/

Statistical test for model organisms association mapping correcting for the confounding from population structure and genetic relatedness. EMMA takes advantage of the specific nature of the optimization problem in applying mixed models for association mapping, which substantially increases the computational speed and the reliability of the results. The current implementation of EMMA is available in an R package. The documentation is included in the installation package.

Proper citation: Efficient Mixed-Model Association (RRID:SCR_008217) Copy   

•   Source: SciCrunch Registry

https://nfregistry.patientcrossroads.org/

A patient registry to identify people with neurofibromatosis (NF) who are interested in participating in clinical trials, as well as determining the commonality of specific characteristics of NF. The NF Registry is committed to secure methodologies and pioneering research that will lead to improving the health and well-being of individuals and families affected by NF. This registry has been created to collect data on large numbers of people with NF. This has never existed before and will help: * Identify people who may be eligible for clinical trials or other research studies being conducted in the field of NF. New clinical trials are launched each year yet challenges identifying participants too often mean that these studies finish late or never really get started. Today, 80 percent of trials fail to recruit enough volunteers within planned timelines. Under enrollment is one of the most significant problems facing NF drug development. Together, we can solve it. * Determine the commonality of specific NF characteristics. This will help researchers and doctors devise better ways to care for people with NF If you or your child has been diagnosed with neurofibromatosis (NF) please join the NF Registry today. It''s quick, it''s easy, and it matters. The key to treatments lies within you researchers can''t deliver treatments without committed volunteers.

Proper citation: NF Registry (RRID:SCR_006277) Copy   

•   Source: SciCrunch Registry

http://www.emedicinehealth.com/dementia_due_to_hiv_infection/article_em.htm

A narrative resource that provides a wealth of information on topic including: * Dementia Due to HIV Infection Overview * Dementia Due to HIV Infection Causes * Dementia Due to HIV Infection Symptoms * Exams and Tests * Dementia Due to HIV Infection Treatment * Self-Care at Home * Medical Treatment * Next Steps * Follow-up * Prevention * Outlook * Support Groups and Counseling * For More Information * Web Links * Multimedia * Synonyms and Keywords Additional information includes: * HIV AIDS Myths and Facts Slideshow Pictures * Take the HIV/AIDS Quiz * AIDS Retrospective Slideshow Pictures

Proper citation: emedicinehealth: Dementia Due to HIV Infection (RRID:SCR_004566) Copy   

•   Source: SciCrunch Registry

http://www.medtronic.com/

Medical technology company that develops and manufactures devices and therapies to treat more than 30 chronic diseases, including heart failure, Parkinson's disease, urinary incontinence, Down syndrome, obesity, chronic pain, spinal disorders, and diabetes. A Commercial healthcare organization for both patients and healthcare professionals. For professionals, it provides products, therapy and procedure solutions, and services.

Proper citation: Medtronic (RRID:SCR_003988) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/tools/cobalt/cobalt.cgi?link_loc=BlastHomeAd

COBALT is a multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST. Pairwise constraints are then incorporated into a progressive multiple alignment. A Linux executable for COBALT, and CDD and PROSITE data used is available at ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/cobalt/ COBALT has reasonable runtime performance and alignment accuracy comparable to or exceeding that of other tools for a broad range of problems.

Proper citation: COBALT: Constraint-based Multiple Alignment Tool (RRID:SCR_004152) Copy   

•   Source: SciCrunch Registry

https://pmsiregistry.patientcrossroads.org/

International registry that consolidates information from individuals with Phelan-McDermid Syndrome into a single database, which will be utilized by researchers to understand Phelan-McDermid Syndrome better. In order to accelerate translational efforts (moving from basic laboratory research to meaningful health outcomes, such as therapies and treatments) related to Phelan-McDermid Syndrome, PMSF is funding the Phelan-McDermid Syndrome International Registry. The Registry is important for characterizing and understanding the syndrome better. Not only will the Registry provide valuable information for families and doctors to make the best care decisions possible, it will be important to help researchers decide what are the most important challenges to address. The Registry will also help scientists find out if there are any PMS patients who might be a good match for their research studies. Collecting information from PMS patients is very important, but protecting the privacy of people affected by PMS is also extremely important. In order to protect your privacy, Patient Crossroads (the company that designed the registry software) has designed many safeguards. Your child''s information will be de-identified so no one who looks at the data can identify you or your child. Your child''s information will be assigned a code. If a researcher is interested in learning more about your child, the researcher will ask the Patient Crossroads/PMSIR genetic counselor to contact you. A scientist will not be able to receive any identifying information about your child unless you give explicit consent for your child''s identity to be released to that researcher. BE PART OF OUR INTERNATIONAL REGISTRY The Registry will provide valuable information for families and doctors to make the best care decisions possible, and it will help researchers decide what are the most important challenges to address in PMS. Establishing the registry addresses two important scientific needs. First, scientists studying PMS need accurate, firsthand information to understand how PMS affects people. Second, scientists who are ready to start studies, such as those that test new treatments, will be able to access The Registry to identify people that may be eligible to participate in studies. In either case, your privacy is assured while the cause of research is advanced. While raw data about PMS will be available to scientists, they won''t have access to any identifying information about your child unless you agree to have your child''s identity released.

Proper citation: Phelan-McDermid Syndrome International Registry (RRID:SCR_004230) Copy   

•   Source: SciCrunch Registry

http://journal.code4lib.org/

This article is an appeal to technically-oriented library staff to initiate collaborative, bottom-up data-analysis efforts across their libraries. We discuss successful strategies used at North Carolina State University (NCSU) Libraries for initiating cross-departmental outreach for data-analysis work, as well as structuring and storing data, and disseminating findings. We present several specific examples of collaborative data-analysis projects undertaken at NCSU Libraries. Although the primary goal of the Code4Lib Journal is to provide practical solutions for technologists working in libraries, it has a lot to offer non-technologists. Technology affects all of the work that our libraries are doing and will define what the future of libraries will look like.

Proper citation: Code4Lib Journal (RRID:SCR_004687) Copy   

•   Source: SciCrunch Registry

https://neuinfo.org/mynif/search.php?q=*&t=literature

Simultaneous search across multiple literature indices, including PubMed and Open Access literature, it is one of the core resources of NIF accessed through the NIF search interface. Literature results are displayed under the Literature tab. Features: * Facet by Year, Author, and / or Journal * Option to search open access literature only * Sort by relevance or year * Snippets from the full text of the paper are included in search results where search term was found * LinkOuts are now provided for some papers. These mean that someone associated a reagent, piece of data, note/blog, etc., with this specific publication. * Searching within sections of articles is now possible within the open access literature. For more info, see, http://neuinfo.org/about/release_notes_4.5.shtm#search. * Annotate papers. Any user can submit a public comment or annotation of an open access paper through the DOMEO tool. For more information, see http://neuinfo.org/about/release_notes_4.5.shtm#annotate

Proper citation: NIF Literature (RRID:SCR_005401) Copy   

•   Source: SciCrunch Registry

https://donatelifela.org

Donate Life Louisiana saves and enhances lives, and positively impacts the donor registry through education, awareness and leadership. Register to Become an Organ, Eye and Tissue Donor.

Proper citation: Donate Life Louisiana (RRID:SCR_005800) Copy   

•   Source: SciCrunch Registry

http://americaninstituteofstress.org/interviews/

From time to time the Editor of Health and Stress interviews leaders in the field of stress management on a variety of topics for inclusion in our publications. Some interviews are listed below. For a complete list of interviews and content, you must be a member of AIS and access the Archives.

Proper citation: American Institute of Stress Interviews (RRID:SCR_005420) Copy   

•   Source: SciCrunch Registry

http://publications.nigms.nih.gov/computinglife/

An NIGMS magazine that showcases the exciting ways that scientists are using the power of computers to expand our knowledge of biology and medicine. From text messaging friends to navigating city streets with GPS technology, we''re all living the computing life. But as we''ve upgraded from snail mail and compasses, so too have scientists. Computer advances now let researchers quickly search through DNA sequences to find gene variations that could lead to disease, simulate how flu might spread through your school and design three-dimensional animations of molecules that rival any video game. By teaming computers and biology, scientists can answer new and old questions that could offer insights into the fundamental processes that keep us alive and make us sick. This booklet introduces you to just some of the ways that physicists, biologists and even artists are computing life. Each section focuses on a different research problem, offers examples of current scientific projects and acquaints you with the people conducting the work. You can follow the links for online extras and other opportunities to learn aboutand get involved inthis exciting new interdisciplinary field.

Proper citation: NIGMS Computing Life (RRID:SCR_005850) Copy   

•   Source: SciCrunch Registry

http://www.ataxia.org/research/patient-registry.aspx

A portal presenting the patient registries and databases of the National Ataxia Foundation. The registries include: Ataxia Patient Registry at CoRDS, Friedreich's Ataxia Research Alliance Patient Registry; the Fragile X Research Registry; Autosomal recessive spastic ataxia of Charlevoix-Saguenay ARSACS; and, Ataxia-Telangiectasia (A-T) Children's Project Family Data Base.

Proper citation: National Ataxia Foundation Patient Registries (RRID:SCR_005341) Copy   

•   Source: SciCrunch Registry

http://search.cpan.org/dist/Bio-ToolBox/lib/Bio/ToolBox.pm

Tools for querying and analysis of genomic data. These libraries provide a useful interface for working with bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined regions of interest (epigenetic enrichment, transcription factor binding sites, etc.). This library works with these tables and provides a set of common tools for working with them. Opening and saving common tab-delimited text formats Support for BED, GFF, VCF, narrowPeak files Scoring intervals with datasets from microarray and sequencing ChIPSeq, RNASeq, microarray expression Support for Bam, BigWig, BigBed, wig, and USeq data formats Intersection with other known annotation Works with any genomic annotation in GTF, GFF3, and UCSC formats The libraries provide a unified and integrated approach to analyses. In many cases, they provide an abstraction layer over a variety of different specialized BioPerl and related modules. Instead of writing numerous scripts specialized for each data format (wig, bigWig, Bam), one script can now work with any data format.

Proper citation: BioToolBox (RRID:SCR_015696) Copy   

•   Source: SciCrunch Registry

https://github.com/ABCD-STUDY/numerical-fitting

Software for a numerical computation library that performs numerical calculations. Used in ABCD study.

Proper citation: numerical-fitting (RRID:SCR_016025) Copy   

•   Source: SciCrunch Registry

https://github.com/csb-toolbox/CSB

Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses.

Proper citation: Computational Structural Biology Toolbox (RRID:SCR_016065) Copy   

•   Source: SciCrunch Registry