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Spinal Research committed to funding international research into cure for spinal cord paralysis. Charity that funds medical research for treating and curing spinal cord paralysis. Supports basic science, clinical research and funds PhD students. ISRT also hosts Annual Network Meetings.

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• SciCrunch
• 17 years ago - by Anonymous

A genetic testing company for rare and complex disorders and syndromes. The company specializes in retinal disorders, reproductive medicine and oncology. They also offer custom genotyping services.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 10,2026. English translation of Andreas Vesalius' Renaissance anatomical atlas On the Fabric of the Human Body (1543, 1555) and an explanation of the work in progress at Northwestern University to translate and annotate this historic work (by Daniel Garrison and Malcolm Hast). This detailed account of human anatomy transformed its subject and forever changed medical education in the West. Its woodcut illustrations became the basis of medical art and illustrations for generations to come, and continue to influence the way we look at the human body. * Book One -- The things that sustain and support the entire body, and what braces and attaches them all. (the bones and the ligaments that interconnect them) * Book Two -- All the ligaments and muscles, instruments of voluntary and deliberate motion * Book Three -- The series of veins and arteries throughout the body * Book Four -- The nerves * Book Five -- The organs of nutrition and generation * Book Six -- The heart and organs serving the heart (Chiefly the heart and lungs) * Book Seven -- The brain and organs of sense Note: Only introduction, images, and essays appear to be available.

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• SciCrunch
• 15 years ago - by Anonymous

An information retrieval system that provides knowledge enriched searching facilities across the ever growing MEDLINE collection, the world's most comprehensive source of life sciences and biomedical bibliographic information. The semantic faceted search, using named entity recognition, can be accessed from your browser. By combining a selection of software services they can provide enhanced results through a process that identifies key entities within the text, such as gene names or proteins, and improves the querying method with unique identifiers by automatically including synonyms, spelling variants and even disambiguating acronyms. This combines with the traditional features found in other interfaces to provide a much needed solution to the growing problem of finding valuable information within the ever increasing volume of modern publications. The current available categories: * PROTEIN, GENE, METABOLITE, DISEASE, SYMPTOM, ORGAN, * DIAG_PROC, THERAPEUTIC_PROC, (diagnostic/therapeutic procedure, e.g. MRI, cerebral blood flow) * GENERAL_PHENOM, HUMAN_PHENOM, NATURAL_PHENOM, (Medical phenomenon or process, e.g. UV radiation ) * INDICATOR (Reagent or diagnostic aid, e.g. hydrogen peroxide, sulfhydryl reagent) * ACRONYM, AUTHOR, PUBLICATIONTYPE (e.g. Journal Article, Technical Report) Reference: C. Nobata, P. Cotter, N. Okazaki, B. Rea, Y. Sasaki, Y. Tsuruoka, J. Tsujii and S. Ananiadou. Kleio: a knowledge-enriched information retrieval system for biology. In Proc. of the 31st Annual International ACM SIGIR Conference, pp. 787--788, 2008

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• SciCrunch
• 16 years ago - by Anonymous

The SWAN (Semantic Web Applications in Neuromedicine) ontology is an ontology for modeling scientific discourse and has been developed in the context of building a series of applications for biomedical researchers, as well as extensive discussions and collaborations with the larger bio-ontologies community. Developing cures for highly complex diseases, such as neurodegenerative disorders, requires extensive interdisciplinary collaboration and exchange of biomedical information in context. Our ability to exchange such information across sub-specialties today is limited by the current scientific knowledge ecosystem's inability to properly contextualize and integrate data and discourse in machine-interpretable form. This inherently limits the productivity of research and the progress toward cures for devastating diseases such as Alzheimer's and Parkinson's. The SWAN ontology is organized in three types of modules: * basic: basic modules represent the ontology building blocks. They cover topics that are general enough to be included in every ontology distribution. The current basic modules are: ** collections ** provenance, authoring and versioning (PAV) ** discourse relationships ** FOAF (in OWL-DL) ** SKOS (in OWL-DL) ** qualifiers ** scientific discourse * extension: extensions modules are covering topics (a) that can be related only to some fields of science (b) for which there could be more than one implementation (c) for which a temporary solution has been provided and it is possible to forecast its substitution. The current extensions modules are: ** life science entities ** citations ** qualifiers extension modules * distribution: distributions are modules that are including all the basic modules and extensions necessary for serving a specific domain (i.e. the SWAN ontology for the Alzheimer knowledge base or the generic distribution that is not binded to any specific scientific domain). The current available distributions are: ** swan-scientific-discourse ** swan-alzheimer

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• SciCrunch
• 15 years ago - by Anonymous

The Analytical and Resource Core provides services and resources to the scientific research community in areas including hematology, clinical chemistry, genetics, immunology, endocrinology, flow cytometry, and pathogen detection. Available resources include biological specimens, viral stocks, DNA, and species-specific reagents. Scientists and staff associated with each of the seven Core Laboratories provide consultation in experimental design, sample collection, and data analysis, and offer assays that utilize species-specific reagents wherever possible. Core Laboratory scientists can also work with users to develop new assays to meet research needs. Training is available for all assays, and Core Laboratories equipment can be made available, typically on a recharge basis. Nonhuman primate resources developed at CNPRC are available to qualified individuals via the Resource Services component of the Core. * Clinical Laboratory * Endocrine Core Laboratory * Flow Cytometry Core Laboratory * Genetics Core Laboratory * Infectious Diseases Immunology Core Laboratory * Pathogen Detection Core Laboratory * Respiratory Disease Immunology Core Laboratory * Affiliated Laboratory: Clinical Proteomics Core Laboratory * Affiliated Laboratory: Microarray Core Facility * Resource Services: The following research resources of CNPRC are available to scientists on a recharge basis. ** Allergen: Characterized protein extracts of house dust mite (Dermatophagoides pteronyssinus and Dermatophagoides farinae) are available for allergen sensitization projects. ** Biological Specimens: Tissues collected at necropsy are available from rhesus monkeys (Macaca mulatta), cynomolgus monkeys (Macaca fascicularis), and titi monkeys (Callicebus cupreus). Contact: Biospecimens (at) primate.ucdavis.edu Blood samples are available through our blood donor program. ** Data: Data for colony animals are available from our computerized database. Data include birth records, weights, reproductive history, relocation history, etc. ** DNA: DNA extracted from peripheral blood mononuclear cells is available on animals of all age-sex classes from known pedigrees. ** Reagents and Samples: Reagents, controls, and known/unknown samples are available from the Pathogen Detection Core Laboratory. Samples include pedigreed sera/plasma, fixed tissues and DNA from macaques and various other species. Validated reagents for many pathogens are available, including SIV, SRV1-5, SFV, STLV, RRV, RhCMV, Herpes B, SV40, and LCV. More information is available at: http://pdl.primate.ucdavis.edu/PDLreagents.html. ** Shipping: Shipping services are available by trained staff who can properly document, package and ship critical experimental materials, including nonhuman primate samples. Assistance is also provided for obtaining CITES permits, required for international shipment of any nonhuman primate samples. ** Transformed B-Cell Lines: Cryopreserved Herpes papio - transformed B cell lines from over 300 rhesus monkeys in the CNPRC colony are available. Transformation of macaque B cells to establish a new cell line is available on request. ** Virus Stock: Rhesus Cytomegalovirus: A unique primary isolate, developed at CNPRC, is available. ** Virus Stock: Simian Immunodeficiency Virus: Aliquots of SIVmac251 and SIVmac239 virus stocks were prepared by propagation in peripheral blood mononuclear cells from rhesus macaques and contain approximately 100,000 50% tissue culture infectious doses per ml. As measured by the commercial SIV branched chain assay, SIVmac251 contains 2 x 109 copies of SIV RNA per ml and SIVmac239 contains 109 copies of SIV RNA per ml. These virus stocks are infectious for rhesus macaques by intravenous, intravaginal and oral routes of inoculation.

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• SciCrunch
• 15 years ago - by Anonymous

Software for short-read mapping to accurately map reads from the next-generation sequencing technology. It can map reads with or without error probability information (quality scores) and supports paired-end reads or bisulfite-treated reads mapping. There is no limitaions on read widths or number of mismatches. RMAP can now map more than 8 million reads in an hour at full sensitivity to 2 mismatches.

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• SciCrunch
• 13 years ago - by Anonymous

Academy scientists, journalists, adventurers and other staff members are blogging their stories and inviting questions and comments. Read current science news, hear from researchers in the field (Philippines, Sao Tome, Papua New Guinea), ask a question of an Academy naturalist, and much more.

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• SciCrunch
• 15 years ago - by Anonymous

PyNIfTI is no longer actively developed. At has been superseded by NiBabel -- a pure-Python package that provides everything that PyNIfTI could do, and a lot more. The PyNIfTI module is a Python interface to the NIfTI I/O libraries. Using PyNIfTI, one can easily read and write NIfTI and ANALYZE images from within Python. The NiftiImage class provides pythonic access to the full header information and for a maximum of interoperability the image data is made available via NumPy arrays.

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• SciCrunch
• 13 years ago - by Anonymous

A Java-based tool to easily find unknown genes in a network that are significantly associated with user-defined target Gene Ontology (GO) categories. PiNGO is implemented as a plugin for Cytoscape, a popular open source software platform for visualizing and integrating molecular interaction networks. PiNGO predicts the categorization of a gene based on the annotations of its neighbors, using the enrichment statistics of its sister tool BiNGO. Networks can either be selected from the Cytoscape interface or uploaded from file. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

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• SciCrunch
• 15 years ago - by Anonymous

A software pipeline based on TopHat2 combined with a splice junction detection algorithm.

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• SciCrunch
• 12 years ago - by Anonymous

A five-year prospective cohort study following 240 patients who have autosomal-dominant polycystic kidney disease (PKD) to determine whether changes in anatomic characteristics of their kidneys as measured by magnetic resonance imaging will be useful in providing surrogate measures for disease progression. CRISP's overall goal is to develop methods that would facilitate shortening the observation period necessary to determine efficacy of treatment interventions in PKD patients. Specific goals of this study are to: * Quantify cyst growth and ascertain severity of renal parenchymal involvement by sequential measurement of total kidney volume and the ratio of intact parenchyma to renal parenchyma occupied by cysts over time * Establish useful clinical correlations of imaging data with other markers of disease progression * Identify and test other potential markers or indices of disease progression, for example, assessment of loss of heterozygosity of renal cells shed in the urine, or other markers, in cohorts of patients with PKD * Gain information about the cost-effectiveness, patient acceptability, and advantages and disadvantages of different imaging techniques used serially in patients with PKD. Some experience has been gained in establishing that repeat imaging of the same PKD patient, using these techniques, yields reproducible estimates of kidney size and the proportion of renal parenchyma occupied by cysts. MRI may also have the advantage of permitting simultaneous estimation of GFR. Ultrasound has the advantage of being more cost-effective and perhaps more acceptable to patients for repetitive studies, but the measurements may be less accurate and reproducible. Nonetheless, there is very limited experience in applying these techniques to follow progression of the renal disease. Development of improved, reproducible imaging methods that assess cyst growth and provide markers of disease progression could markedly improve the feasibility of clinical trials. Participating clinical centers are Emory University, the Mayo Clinic, University of Kansas, and the University of Alabama at Birmingham. The data coordinating and imaging analysis center is at Washington University. (PI has since moved to University of Pittsburgh) The study found that kidney enlargement resulting from the expansion of cysts is continuous, quantifiable, and associated with the decline of renal function. Cystic expansion occurs at a consistent rate per individual, although it is heterogeneous in the population, and that larger kidneys are associated with more rapid decrease in renal function. These anatomic characteristics of patient kidneys may provide useful surrogate measures for disease progression, and hence enhance the development of targeted therapies for autosomal dominant PKD. CRISP III is a five-year prospective cohort study to follow ~170 remaining autosomal dominant polycystic kidney disease (ADPKD) patients who were part of the original CRISP cohort study. CRISP III will verify and extend the preliminary observations of CRISP to determine the extent to which quantitative (kidney volume and blood flow, and hepatic and kidney cyst volume) or qualitative (cyst distribution and character) structural parameters predict renal insufficiency and develop and test new metrics to quantify and monitor disease progression. Urine metabolites and the genome will be correlated with the progression of disease to look for new, predictive disease biomarkers. This information from CRISP III will help determine if the kidney enlargement, blood flow, cyst distribution, or urine metabolites can function as an informative surrogate measure for disease progression.

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• dkNET
• 14 years ago - by Anonymous

Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

An online tool for the analysis of bisulfite sequencing DNA methylation data. The software has specificity and quality control functions that allow the user to compile a set of sequences.

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• SciCrunch
• 13 years ago - by Anonymous

Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.

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• SciCrunch
• 13 years ago - by Anonymous

Blog about technology, molecular biology, and editorial comments on the current state of science on the internet. Brian Krueger PhD, is the owner, creator and coder of LabSpaces by night and a Molecular biologist by day. His posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, his employer, or his educational institution.

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• SciCrunch
• 14 years ago - by Anonymous

Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. A European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Annotated list of online CME (continuing medical education) with links to, and descriptions of, Web Sites offering courses and CME credit specifically aimed at Canadian physicians. All Canadian Online CME offering MainPro-M1 credit includes an online group discussion format. You must participate in these discussions as well as go though the didactic material to earn credit.

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• SciCrunch
• 17 years ago - by Anonymous

A software tool for removal of de novo duplicates in paired short DNA sequences.

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• SciCrunch
• 13 years ago - by Anonymous