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http://www.jcamp-dx.org/

An International Union of Pure and Applied Chemistry (IUPAC) subcommittee that deals with individual projects related to technique-specific data standards as well as generic issues. There are worrying gaps in the coverage of known chemistry by reference spectroscopic databases, which are unlikely to be filled by the activities of the commercial sector alone. The IS-DB offers the scientific community the opportunity to share their spectra and develop a vital resource for future generations. Such a collection of spectra will help to provide significant improvements in human health, new materials, environmental protection, sustainable development and educational progress. XML in Chemistry is a new IUPAC initiative to bring a degree of regulation to this important and rapidly expanding field. They aim to facilitate the validation of data dictionaries for various groups developing ontologies expressed in XML in the broad field of Chemistry. This will help to reduce duplication of effort around the world and allow development projects to build on the work previous groups concentrating on their own innovative goals rather than wasting time and effort re-inventing wheels. IUPAC encourages the submission of projects in all areas of chemistry relevant to its work. If you believe there is a need for a new scientific data standard in your field and wish to know more about how to form a limited term task group to get the standard developed please contact the subcommittee.

Proper citation: IUPAC CPEP Subcommittee on Electronic Data Standards (RRID:SCR_005082) Copy   

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http://krasnow1.gmu.edu/cn3/hippocampus3d/

Data files for a high resolution three dimensional (3D) structure of the rat hippocampus reconstructed from histological sections. The data files (supplementary data for Ropireddy et al., Neurosci., 2012 Mar 15;205:91-111) are being shared on the Windows Live cloud space provided by Microsoft. Downloadable data files include the Nissl histological images, the hippocampus layer tracings that can be visualized alone or superimposed to the corresponding Nissl images, the voxel database coordinates, and the surface rendering VRML files. * Hippocampus Nissl Images: The high resolution histological Nissl images obtained at 16 micrometer inter-slice distance for the Long-Evans rat hippocampus can be downloaded or directly viewed in a browser. This dataset consists of 230 jpeg images that cover the hippocampus from rostral to caudal poles. This image dataset is uploaded in seven parts as rar files. * Hippocampus Layer Tracings: The seven hippocampus layers ''ML, ''GC'', ''HILUS'' in DG and ''LM'', ''RAD'', ''PC'', ''OR'' in CA were segmented (traced) using the Reconstruct tool which can be downloaded from Synapse web. This tool outputs all the tracings for each image in XML format. The XML tracing files for all these seven layers for each of the above Nissl images are zipped into one file and can be downloaded. * Hippocampus VoxelDB: The 3D hippocampus reconstructed is volumetrically transformed into 16 micrometer sized voxels for all the seven layers. Each voxel is reported according to multiple coordinate systems, namely in Cartesian, along the natural hippocampal dimensions, and in reference to the canonical brain planes. The voxel database file is created in ascii format. The single voxel database file was split into three rar archive files. Please note that the three rar archive files should be downloaded and decompressed in a single directory in order to obtain the single voxel data file (Hippocampus-VoxelDB.txt). * 3D Surface Renderings: This is a rar archive file with a single VRML file containing the surface rendering of DG and CA layers. This VRML file can be opened and visualized in any VRML viewer, e.g. the open source software view3dscene. * 3D Hippocampus Movie: This movie contains visualization of the 3D surface renderings of CA (blue) and DG (red) inner and outer boundaries; neuronal embeddings of DG granule and CA pyramidal dendritic arbors; potential synapses between CA3b interneuron axon and pyramidal dendrite, and between CA2 pyramidal axon and CA pyramidal dendrites.

Proper citation: Hippocampus 3D Model (RRID:SCR_005083) Copy   

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http://www.iupac.org/

Recognized as the world authority on chemical nomenclature, terminology, standardized methods for measurement, atomic weights and many other critically evaluated data, this scientific, international, non-governmental and objective body addresses many global issues involving the chemical sciences. It serves to advance the worldwide aspects of the chemical sciences and to contribute to the application of chemistry in the service of Humankind. The Union sponsors major international meetings that range from specialized scientific symposia to CHEMRAWN meetings with societal impact. * Projects: IUPAC encourages the submission of projects in all areas of chemistry relevant to its work. * Publications: IUPAC publishes books, journals, electronic resources, and issues many reports in all areas of chemistry * Conferences: Each year IUPAC sponsors a large number of symposia that cover a wide range of specialized topics in chemistry. * Members and bodies: Chemists throughout the world are engaged on a voluntary basis in the scientific work of IUPAC.

Proper citation: IUPAC (RRID:SCR_005084) Copy   

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http://www.science3point0.com/

Science 3.0 is a community for the advancement of online science. Science 3.0 is constantly trying to use and develop web 2.0 tools to make online science more efficient. Community projects include FigShare, COASPedia, ScienceSeeker, and Science 3.0 Open Data. Science 3.0 combines the hypothesis based inquiry of laboratory science with the methods of social science research to understand and improve the use of new human networks made possible by today''s digital connectivity. This website is a community where those interested in the advancement of research can share ideas, tools and build connections. This website is designed to be a neutral, impartial community where people can discuss the pros and cons of each application so that they can be developed in the most efficient manner. The site is not designed to be a place where all science researchers from all disciplines meet and share results. The site is for those who wish to develop science online, or have an interest in science online. We do not have the answers to all of the problems associated with open access and bringing science to the masses. We are the place where like minded people can collaborate to generate these answers.

Proper citation: Science 3.0 (RRID:SCR_005216) Copy   

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http://www.broadinstitute.org/software/pathseq/

A computational tool for the identification and analysis of microbial sequences in high-throughput human sequencing data that is designed to work with large numbers of sequencing reads in a scalable manner. This process is composed of a subtractive phase in which input reads are subtracted by alignment to human reference sequences, and an analytic phase in which the remaining reads are aligned to microbial reference sequences (viral, fungal, bacterial, archaeal) and de novo assembled. PathSeq is currently available in a cloud computing environment via Amazon Web Services The typical approach one would take to pathogen discovery with PathSeq: RNA or DNA is extracted from the tissue of interest and sequencing libraries are constructed to be run on the next-generation DNA sequencing platform of choice. The resulting sequence data is run through the PathSeq pipeline in a cloud computing environment. PathSeq reports potential microbes in the sequence data as well as the complete set of reads that could not be identified as human or microbial sequences.

Proper citation: PathSeq (RRID:SCR_005203) Copy   

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http://cbrc.kaust.edu.sa/readscan/

A highly scalable parallel software program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets.

Proper citation: READSCAN (RRID:SCR_005204) Copy   

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http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html

An algorithmic software tool for detecting known viruses and their integration sites using next-generation sequencing of human cancer tissue. VirusSeq takes FASTQ files (paired-end reads) as input.

Proper citation: VirusSeq (RRID:SCR_005206) Copy   

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http://sourceforge.net/projects/hivcd/

Informatics software tool to identify patient sequences that are too similar to happen by chance alone. Highly similar sequences are likely to occur from contamination or other situations like geographic linkage.

Proper citation: HIVCD (RRID:SCR_005201) Copy   

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http://www.lsrf.org/

In the belief that innovation and discovery occur in direct proportion to quality of training, the Life Sciences Research Foundation administers an international program of postdoctoral fellowships in all areas of the life sciences. Since it was established, in 1981, the Foundation has attracted support from a wide variety of sponsors. The mission of the Life Sciences Research Foundation (LSRF) is to establish partnerships between those who support research in the life sciences and academic institutions for their mutual benefit. The simple vehicle for achieving this partnership is a highly competitive postdoctoral fellowship program. Fellowship Eligibility. Three-year fellowships will be awarded on a competitive basis to graduates of medical and graduate schools in the biological sciences holding M.D., Ph.D., D.V.M. or D.D.S. degrees. Awards will be based solely on the quality of the individual applicant''s previous accomplishments, and on the merit of the proposal for postdoctoral research. Persons doing a second postdoc are eligible only if they are transferring to a different supervisor''s laboratory and embarking on a new project not connected to their previous research. All U.S. citizens are eligible to apply with no geographic restriction on the laboratory of their choice. Foreign applicants will be eligible for study in U.S. laboratories. LSRF fellows must carry out their research at nonprofit institutions. LSRF fellows may change projects, laboratories, and/or institutions during the fellowship as long as the eligibility rules listed here are not violated. A person holding a faculty appointment is not eligible to apply for an LSRF fellowship. The LSRF solicits monies from industry, foundations and individuals to support postdoctoral fellowships in the life sciences. Active solicitation of funds continues, for which we need the assistance of all concerned individuals. We recognize that discoveries and the application of innovations in biology for the public''s good will depend upon the training and support of the highest quality young scientists in the very best research environments. LSRF awards fellowships across the spectrum of the life sciences: biochemistry; cell, developmental, molecular, plant, structural, organismic population and evolutionary biology; endocrinology; immunology; microbiology; neurobiology; physiology; virology. Note: There may be no more than one LSRF fellow in any one laboratory at a time.

Proper citation: Life Sciences Research Foundation (RRID:SCR_005115) Copy   

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https://www.huck.psu.edu/graduate-programs/neuroscience

Program provides preparation for students seeking careers in academia, education and industry. Students are usually admitted with the intent of obtaining a PhD degree in Neuroscience but the MS degree may be sought as part of the doctoral program.

Proper citation: Pennsylvania State University Huck Institutes of the Life Sciences Neuroscience Graduate Program (RRID:SCR_004941) Copy   

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http://archive.gersteinlab.org/proj/rnaseq/IQSeq/

Software for integrated Isoform Quanti?cation Analysis based on A Partial Sampling Framework.

Proper citation: IQSeq (RRID:SCR_005238) Copy   

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http://elderaffairs.state.fl.us/english/alz.php

A program that provides services to meet the needs of individuals with Alzheimer's disease, and similar memory disorders, and their families. The Alzheimer's Disease Initiative (ADI) of Florida provides caregiver respite services and support which include in-home, facility-based, emergency, and extended care for caregivers who serve patients with memory disorders. Additionally, the ADI includes services provided by Memory Disorder Clinics (MDCs).

Proper citation: State of Florida Alzheimer's Disease Initiative (RRID:SCR_004942) Copy   

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http://bioinformatics.engineering.asu.edu/springs/Sprouts/index.html

SPROUTS is a database of predicted protein folding related data. It was designed to gather all the results from a study concerning the comparison between tools devoted to the prediction of stability changes upon point mutations. The second aim of this database is to offer simple and user-friendly tools to better visualize and analyze the results obtained. We are now able to propose three ways of visualization and analysis: the first one consists in getting raw Delta Delta G values in a table. The second one is a 2D graph representation of a computed stability score for each residue of a given sequence and for each tool. The last one is based on a Jmol applet (Jmol) with the possibility to represent the 3D structure of a given protein with symbols representing the information stored in the database. We assume that each visualization mode offers a different look on the data stored in the database and will suit to every scientists willing to query the database whether they are more used to handle 3D protein structure or 1D/2D sequence problems. Finally, the ultimate objective is to integrate these data and their analysis with other structural bioinformatic concepts in order to improve other methods that may be related to this concept. We are currently working at adding the information extracted from our other projects related to the prediction of protein folding nucleus in order to obtain a meta server devoted to the characterization of the folding core of proteins. As of today, this database has grown up and consists in more than 100 structures which have been computed for a total of around 16500 amino acids.

Proper citation: SPROUTS- Structural Prediction for Protein Folding Utility System (RRID:SCR_005118) Copy   

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http://helmsleytrust.org/program-areas/health-medical-research/

The Leona M. and Harry B. Helmsley Charitable Trust supports a broad spectrum of healthcare and medical research-based programs. The areas supported include Type 1 Diabetes, Digestive Diseases, Rural Healthcare, Cardiology, and a range of other programs and institutions.

Proper citation: Helmsley Charitable Trust (RRID:SCR_005111) Copy   

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http://compbio.cs.toronto.edu/ireckon/

An algorithm for the simultaneous isoform reconstruction and abundance estimation. In addition to modelling novel isoforms, multi-mapped reads and read duplicates, this method takes into account the possible presence of unspliced pre-mRNA and intron retention. iReckon only requires a set of transcription start and end sites, but can use known full isoforms to improve sensitivity. Starting from the set of nearly all possible isoforms, iReckon uses a regularized EM algorithm to determine those actually present in the sequenced sample, together with their abundances. iReckon is multi-threaded to increase efficiency in all its time consuming steps.

Proper citation: iReckon (RRID:SCR_005232) Copy   

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http://www.hfsp.org/funding

The HFSP supports novel, innovative and interdisciplinary basic research focused on the complex mechanisms of living organisms; topics range from molecular and cellular approaches to systems and cognitive neuroscience. A clear emphasis is placed on novel collaborations that bring biologists together with scientists from fields such as physics, mathematics, chemistry, computer science and engineering to focus on problems at the frontier of the life sciences. The Trust provides funding for research regarding complex biological systems. It offers research grants, post doc fellowships, career development fellowships, and short- long- and cross- disciplinary fellowships. HFSP funding programs are strictly project-related and begin at the postdoctoral level. We have no support for PhD students nor for travel grants to scientific meetings. Nor do we provide sponsorship or funds to organizers of scientific meetings. Research Grants Research Grants are awarded for novel collaborations involving extensive collaboration among teams of scientists working in different countries and in different disciplines. Two types of grants are available: Young Investigators Grants and Program Grants. Postdoctoral Fellowships Postdoctoral Fellowships are available for scientists who wish to work in foreign laboratories, with emphasis on individuals early in their careers who wish to obtain training in a different field of research. Fellows who return to their home countries or move to an HFSP member country that is different from the Fellowship host country are eligible to apply for a Career Development Award. Long-Term Fellowships are for scientists with a Ph.D. degree in the life sciences who wish to broaden their experience through postdoctoral training abroad. Cross-Disciplinary Fellowships are intended for postdoctoral fellows with a Ph.D. degree in the physical sciences, chemistry, mathematics, engineering and computer sciences who wish to receive training in biology. Career Development Awards Career Development Awards are for former HFSP Long-Term or Cross-Disciplinary Fellows who return to their home country or move to an HFSP member country that is different from the host country of their HFSP Fellowship. The award provides support for initiating the fellows'' first independent laboratory., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Human Frontier Science Program (RRID:SCR_005112) Copy   

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http://elderaffairs.state.fl.us/doea/BrainBank/index.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A service and research oriented network of statewide regional brain bank sites. The intent of the brain bank program is to study brains of persons clinically diagnosed with dementia and provide tissue for research after their deaths. Mt. Sinai Medical Center contracts annually with the State of Florida to operate the primary brain bank. Coordinators at regional brain bank sites in Orlando, Tampa and Pensacola assist in recruiting participants and act as liaisons between the brain bank and participant families. Alzheimer's disease respite care program providers, memory disorder clinics, and model day care programs also recruit brain bank participants. The Florida Brain Bank supports collaborative research programs related to Alzheimer's disease and other degenerative disorders of the brain.

Proper citation: Florida Brain Bank (RRID:SCR_004936) Copy   

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http://gmt.genome.wustl.edu/somatic-sniper/current/

Software program to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255) that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and 255 means there is a probability of 1 ? 10(255/-10) that the genotypes are different between tumor and normal. This is consistent with how the SAM format reports such probabilities. It is currently available as source code via github or as a Debian APT package.

Proper citation: SomaticSniper (RRID:SCR_005108) Copy   

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http://www.braintumorfunders.org/

The Brain Tumor Funders'' Collaborative is a partnership among five private philanthropic and advocacy organizations: American Brain Tumor Association, Brain Tumour Foundation of Canada, Children''s Brain Tumor Foundation, James S. McDonnell Foundation, and Sontag Foundation. This Collaborative promotes research directly relating to brain tumors and offers grants to professors and institutions to conduct research.

Proper citation: Brain Tumor Funders Collaborative (RRID:SCR_005104) Copy   

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

A stand-alone executable software with user-friendly graphical interface implemented in Python/C++ for rare variant association studies. It is designed as a unified simulation framework to provide an unbiased and easy manner to evaluate association methods, including novel methods, under a broad range of choice of biological contexts. It consists of three modules, variant data simulator, genotype/phenotype generator and association method evaluator. SimRare generates variant data for gene regions using forward-time simulation which incorporates realistic population demographic and evolutionary scenarios. For phenotype data it is capable of generating both case-control and quantitative traits. The phenotypic effects of variants can be detrimental, protective or non-causal. SimRare has a graphical user interface which allows for easy entry of genetic and phenotypic parameters. Simulated data can be written into external files in a standard format. For novel association method implemented in R it can be imported into SimRare, which has been equipped built in functions to evaluate performance of new method and visually compare it with currently available ones in an unbiased manner.

Proper citation: SimRare (RRID:SCR_005226) Copy   

•   Source: SciCrunch Registry