Curator Dashboard

Allen Mouse Brain Atlas includes full color, high resolution anatomic reference atlas accompanied by systematic, hierarchically organized taxonomy of mouse brain structures. Enables interactive online exploration of atlas and to provide deeper level of 3D annotation for informatics analysis and viewing in Brain Explorer 3D viewer.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data.

• Resource
• SciCrunch
• 12 years ago - by Anonymous

Table providing information about integral membrane proteins whose crystallographic, or sometimes NMR, structures have been determined to a resolution sufficient to identify TM helices of helix-bundle membrane proteins (typically 4 - 4.5 angstroms). It is based upon Preusch et al. (1998) as revised by White & Wimley (1999). Reference is made to all of the protein types whose structures have been determined. They have attempted to make the database as inclusive as possible.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).

• Resource
• SciCrunch
• 13 years ago - by Anonymous

GpetView is light-weight image viewer based on Gtk+ library. The supported image format is ANALYZE(TM) format (Mayo Foundation ). GpetView can run on Unix-systems, such as Linux, Solaris, IRIX, Mac OS-X etc. From Version 2.0, GpetView can also run on Win32 system, if you have installed Glib and Gtk+(2.x). Glib andGtk+ can be found at http://www.gtk.org. For Windows users, you can find Gtk+ libraries at http://gladewin32.sourceforge.net/modules/news/ GpetView has the following features: * very light-weight * view images as transverse, coronal, or sagittal * change color-map (support Analyze lkup file) * zoom images * ROI (Region-Of-Interest) with shapes of circle, ellipse, rectangle, polygon and automatic edge detection * Image histogram and profile Sponsors: This resource is supported by Osaka University. Keywords: Image, Viewer, Software, Transverse, Coronal, Sagittal, Map, Histogram,

• Resource
• SciCrunch
• 17 years ago - by Anonymous

An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

D-HaploDB genome-wide definitive haplotypes, determined using a collection of 100 Japanese complete hydatidiform moles (CHMs), each carrying a genome derived from a single sperm. The haplotypes incorporate 281 k (D-Haplo Phase I: D1), 581k (D-Haplo Phase II: D2), or 1M (D-Haplo Phase III: D3) SNPs, genotyped with high throughput array-based oligonucleotide hybridization techniques. The Definitive Haplotype Browser can be used to view various information, such as SNP alleles, haplotype blocks, LD-bins and extended shared haplotypes (ESHs) in our study.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

The Trinity Biobank was established in 2005 to serve the needs of researchers in the area of genetic epidemiology, population genetics and pharmacogenomics. Its services are available to researchers not only in Trinity College but to other institutions at home and abroad. We provide an automated DNA extraction service purifying large volumes blood (up to 10mL whole blood) and tissue DNA for archival and other purposes. In addition it makes available purified DNA and associated GWAS data from 2000 healthy donors for research use. A key requirement for reliable downstream use of DNA is purity and strand size. The quality of DNA in blood and tissue deteriorates upon storage without purification even at -80 degrees C. We ensure rapid turnaround of biological samples through automated extraction using the Qiagen Autopure system based on optimized ''salting out'' chemistry. The purified DNA sample may then be stored safely at -20 degrees C without deterioration thus freeing up valuable -80 degree C freezer space and the associated capital and maintenance cost as well as security and lab space provision. Automated DNA extraction is particularly suitable for high-throughput sample processing called for in epidemiological studies or simply for clearing sample inventory backlogs. The Trinity Biobank distributes control DNA to researchers as part of its remit to enhance the level of research activity and to synergize molecular medicine research nationally and internationally. The buffy coat collection has been made possible with the cooperation of the Irish Blood Transfusion Service (IBTS). An important requirement to access the collection is that the use of the samples relates only to ethically-approved research and to specifically-nominated research projects. The DNA collection consists of high quality human genomic DNA. Each of the available 2,000 samples is from a single individual and each sample comes with the age and gender data of the donor. The buffy coat sample is derived from the total white cell compliment (50mL buffy coat) of a blood donation (c 400mL). We will endeavor to fulfill samples number requests based on age and gender as best as possible. This collection has also been genotyped using the Affymetrix Genome-Wide Human SNP Array 6.0, featuring 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation (CNV). The DNA comes available as a 100ng/uL in 100uL of TE Buffer, ie in 10ug amounts in a separate screw-cap ampoule. The ampoules are shipped in 100-tube boxes (Sarstedt). Corresponding plasma (ACD) is also available on request. Genotype data is supplied in PLINK binary PED files format (http://pngu.mgh.harvard.edu/~purcell/plink/ ).

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ''''Gene Set Analysis'''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. A medical center with a neuropathology research program focused on the normal and abnormal aging process of the central nervous system and a funding source for research. The center serves as a collection site for brains in order to study normal aging and neurodegenerative diseases like Alzheimer's.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

A data warehouse that integrates information on patients from multiple sources and consists of patient information from all the visits to Cincinnati Children''''s between 2003 and 2007. This information includes demographics (age, gender, race), diagnoses (ICD-9), procedures, medications and lab results. They have included extracts from Epic, DocSite, and the new Cerner laboratory system and will eventually load public data sources, data from the different divisions or research cores (such as images or genetic data), as well as the research databases from individual groups or investigators. This information is aggregated, cleaned and de-identified. Once this process is complete, it is presented to the user, who will then be able to query the data. The warehouse is best suited for tasks like cohort identification, hypothesis generation and retrospective data analysis. Automated software tools will facilitate some of these functions, while others will require more of a manual process. The initial software tools will be focused around cohort identification. They have developed a set of web-based tools that allow the user to query the warehouse after logging in. The only people able to see your data are those to whom you grant authorization. If the information can be provided to the general research community, they will add it to the warehouse. If it cannot, they will mark it so that only you (or others in your group with proper approval) can access it.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

:GLOM MAP was written for MATLAB, it works equally as well on the PC as on the MAC. GLOM MAP consists of two components: 1. OBS can be used to map the location of glomeruli in transverse sections of the olfactory bulb. 2. GDB can be used to transform the OBS data and to analyze the collected glomerular activity data. This data can be scored and mapped in the radial and anterio-posterior dimensions as discussed in Salcedo et al, 2005. :

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A MATLAB toolbox which uses three dimensional probabilistic cytoarchitechtonic maps to correlate microscopic, anatomic and functional data of the cerebral cortex. Correlating the activation foci identified in functional imaging studies of the human brain with structural (e.g., cytoarchitectonic) information on the activated areas is a major methodological challenge for neuroscience research. We here present a new approach to make use of three-dimensional probabilistic cytoarchitectonic maps, as obtained from the analysis of human post-mortem brains, for correlating microscopical, anatomical and functional imaging data of the cerebral cortex. We introduce a new, MATLAB based toolbox for the SPM2 software package which enables the integration of probabilistic cytoarchitectonic maps and results of functional imaging studies. The toolbox includes the functionality for the construction of summary maps combining probability of several cortical areas by finding the most probable assignment of each voxel to one of these areas. Its main feature is to provide several measures defining the degree of correspondence between architectonic areas and functional foci. The software, together with the presently available probability maps, is available as open source software to the neuroimaging community. This new toolbox provides an easy-to-use tool for the integrated analysis of functional and anatomical data in a common reference space.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Excel files available for download of ranking tables of NIH Funding to US Medical Schools in 2010, school and Principal Investigator (PI) rankings by Medical School Department, direct plus indirect costs (excluding both R & D contracts and American Recovery and Reinvestment Act (ARRA) Awards), etc. Categories under the Basic Science Department and Clinical Science Department are available as well as the rank of each School of Medicine from 2001-2010. The data in the 2010 Award files was obtained from the Research Portfolio Online Reporting Tool (RePORT) from the National Institutes of Health at http://report.nih.gov/award/trends/AggregateData.cfm. The Award Data correspond to the US Government fiscal year. Awards for 2010 correspond to those granted from 1 October 2009-30 September 2010. There is considerable variation on how universities credit awards and how the NIH deals with these variations.

• Resource
• SciCrunch
• 16 years ago - by Anonymous

Research-grade, CRT-replacement LCD display system for vision science and psychophysics. It combines a 22.5″ 1920×1200 industrial LCD (wide 176°/176° viewing angles) with a custom panel/video controller engineered for deterministic stimulus timing and synchronized acquisition. The display supports 12-bit intensity resolution per RGB channel via custom video modes. It uses a scanning RGB LED backlight to improve temporal precision (e.g., crisp frame transitions and reduced motion artifacts) while bypassing consumer “enhancement” processing to keep output predictable for experiments. VIEWPixx also integrates microsecond-synchronized peripherals commonly needed in timing-sensitive paradigms—24-channel TTL I/O (triggers), stereo audio I/O, analog I/O, and a button-box interface—implemented on the same board as the video pipeline for tight hardware-to-video synchronization.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

An Antibody supplier

• Resource
• SciCrunch
• 14 years ago - by Anonymous

A small tool for simulating sequence reads from a reference genome.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome.

• Resource
• SciCrunch
• 13 years ago - by Anonymous