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http://ebhcstrategies.wetpaint.com/

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. This wiki focuses on the process, techniques and tools of high quality searching in the context of evidence-based health care. Information collected in the wiki is primarily intended for medical librarians, but may be of interest to others. Please keep in mind that search strategies and tools here are intended for use by trained professionals in the course of their professional duties, and are not intended for use by the general public. If they are helpful or useful to others that is a plus, but not the primary purpose of the site.

Proper citation: Evidence-Based Health Care Search Strategies (RRID:SCR_010606) Copy   

•   Source: SciCrunch Registry

http://htsvipr.sourceforge.net/

A software program to screen for sequence variants (SNPs, deletions) in sequence data generated by high-throughput-sequencing platforms.

Proper citation: vipR (RRID:SCR_010685) Copy   

•   Source: SciCrunch Registry

http://ascb.org/

The American Society for Cell Biology (ASCB) was founded in 1960 to bring the varied facets of cell biology together. The Society''s purpose is to promote and develop the field of cell biology. Its objectives are achieved through the scholarly dissemination of research at its Annual Meeting and Summer Meetings and in its publications. The ASCB strives to ensure the future of basic scientific research by providing training and development opportunities for students and young investigators, and also by keeping Congress and the American public informed about the importance of biological research. Since its founding, the ASCB has grown to approximately 10,000 members in the United States and more than 65 countries around the world. About 25% of ASCB members are international. Current members come from universities, colleges, professional schools, government, industry, and public and private research institutions. Membership in the ASCB is open to all research scientists, students, educators (high school, undergraduate, and graduate level), and technicians who have education or research experience in cell biology or an allied field.

Proper citation: American Society for Cell Biology (RRID:SCR_010600) Copy   

•   Source: SciCrunch Registry

http://www.ifomis.org/

The Institute for Formal Ontology and Medical Information Science (IFOMIS) comprehends an interdisciplinary research group, with members from Philosophy, Computer and Information Science, Logic, Medicine, and Medical Informatics, focusing on theoretically grounded research in both formal and applied ontology. Its goal is to develop a formal ontology that will be applied and tested in the domain of medical and biomedical information science.

Proper citation: IFOMIS (RRID:SCR_010604) Copy   

•   Source: SciCrunch Registry

http://www.genome.umd.edu/masurca.html

A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MaSuRCA (RRID:SCR_010691) Copy   

•   Source: SciCrunch Registry

http://www.bu.edu/alzresearch/index.html

The goal of the Alzheimers Disease Center is to help reduce the human and economic costs associated with Alzheimers disease through the advancement of knowledge. The primary missions of the Center are to: conduct and facilitate cutting-edge Alzheimers disease research; enhance clinical care for Alzheimers disease patients and their families; and provide education regarding Alzheimers disease to both professional and lay audiences. The Center is made up of a multidisciplinary group of professionals dedicated to research, clinical care, and education.

Proper citation: Boston University Alzheimer's Disease Center (RRID:SCR_010692) Copy   

•   Source: SciCrunch Registry

http://www.lifeextensionfoundation.org/

Established in 1980, the Life Extension Foundation is a nonprofit organization, whose long-range goal is to radically extend the healthy human lifespan by discovering scientific methods to control aging and eradicate disease. The largest organization of its kind in the world, the Life Extension Foundation has always been at the forefront of discovering new scientific breakthroughs for use in developing novel disease prevention and treatment protocols to improve the quality and length of human life. Through its private funding of research programs aimed at identifying and developing new therapies to slow and even reverse the aging process, the Life Extension Foundation seeks to reduce, and ultimately eliminate, such age-related killers as heart disease, stroke, cancer and Alzheimer''s disease. Long-time members are keenly aware of the scientific research that Life Extension Foundation funds to develop validated methods to slow and reverse the aging process. Less known is Life Extension''s multi-prong program to develop safer and more effective cancer therapies. One reason we focus so heavily on cancer research is that this dreaded disease represents a roadblock in our ability to develop effective means to combat aging.

Proper citation: Life Extension Foundation (RRID:SCR_010574) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.research.nicta.com.au/software/gossamer/

A software application for the de novo assembly of genomes from fragments of DNA that specifically attacks the question of scalability.

Proper citation: Gossamer (RRID:SCR_010612) Copy   

•   Source: SciCrunch Registry

http://neurolog.polytech.unice.fr/doku.php?id=neurolog

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The NeuroLOG consortium is addressing: *Management and access of partly structured data, heterogeneous and distributed in an open environment. *Access control and protection of private medical data. *Control of workflows implied in complex computing process on grid infrastructures. *Extraction and quantification of relevant parameters for different pathologies: Multiple sclerosis, Brain Vascular Stroke, Brain tumors Four application pipelines have been proposed in the context of the project. The pipelines are formalized using the Scufl data flow language. *Multiple Sclerosis image analysis pipelines *Brain Stroke application pipeline (from GIN) *Stroke / tumours Anacom application pipeline (from IFR49) Different softwares developed and/or used in this project are presented., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NeuroLOG (RRID:SCR_010582) Copy   

•   Source: SciCrunch Registry

http://www.biodatomics.com/

An open source commercial platform for genomic analysis. Included is a home brewed workflow engine and code provenance tracking, no data provenance tracking. Multiple tools like HMMR and Blast are included in the platform with an architecture that allows others to be plugged in and the code to be modified. Data storage is handled by hadoop clusters.

Proper citation: Biodatomics (RRID:SCR_010464) Copy   

•   Source: SciCrunch Registry

http://pathema.jcvi.org/Pathema/index.html

Pathema is one of the eight Bioinformatics Resource Centers designed to serve as a core resource for the bio-defense and infectious disease research community. Pathema strives to support basic research and accelerate scientific progress for understanding, detecting, diagnosing and treating an established set of six target NIAID Category A-C pathogens: Category A priority pathogens; Bacillus anthracis and Clostridium botulinum, and Category B priority pathogens; Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens and Entamoeba histolytica. Each target pathogen is represented in one of four distinct clade-specific Pathema web resources and underlying databases developed to target the specific data and analysis needs of each scientific community. All publicly available complete genome projects of phylogenetically related organisms are also represented, providing a comprehensive collection of organisms for comparative analyses. Pathema facilitates the scientific exploration of genomic and related data through its integration with web-based analysis tools, customized to obtain, display, and compute results relevant to ongoing pathogen research. Pathema serves the bio-defense and infectious disease research community by disseminating data resulting from pathogen genome sequencing projects and providing access to the results of inter-genomic comparisons for these organisms. The Pathema BRC contract ends in December 2009. At that time JCVI will cease maintenance of the Pathema web resource and data. The PATRIC team, located at the Virginia Bioinformatics Institute, created and maintains a consolidated BRC for all of the NIAID category A-C priority pathogenic bacteria. The EuPathDB team at the University of Pennsylvania will support all eukaryotic pathogens. Pathema transferred all data and software to PATRIC and EuPathDB for incorporation into their new Web-based bioinformatics resource.

Proper citation: Pathema (RRID:SCR_010585) Copy   

•   Source: SciCrunch Registry

http://www.hupo.org/

The Human Proteome Organisation (HUPO) is an international scientific organization representing and promoting proteomics through international cooperation and collaborations by fostering the development of new technologies, techniques and training.

Proper citation: HUPO - Human Proteome Organisation (RRID:SCR_010707) Copy   

•   Source: SciCrunch Registry

http://www.bcgsc.ca/platform/bioinfo/software/abyss

Software providing de novo, parallel, paired-end sequence assembler that is designed for short reads. ABySS 1.0 originally showed that assembling human genome using short 50 bp sequencing reads was possible by aggregating half terabyte of compute memory needed over several computers using standardized message passing system. ABySS 2.0 is Resource Efficient Assembly of Large Genomes using Bloom Filter. ABySS 2.0 departs from MPI and instead implements algorithms that employ Bloom filter, probabilistic data structure, to represent de Bruijn graph and reduce memory requirements.

Proper citation: ABySS (RRID:SCR_010709) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/alfresco/

The aim is to develop a new visualization tool that allows effective comparative genome sequence analysis. The program will compare multiple sequences from putitatively homologous regions in different species. Results from various different existing analysis programs, such as gene prediction, protein homology and regulatory sequence prediction programs shall be visualized and used to find corresponding sequence domains. The program functions as an stand-alone application and also over the World Wide Web. With this in mind it is being developed using the Java programming language. A key feature of the program is to use available analysis programs relevant to comparative genome sequence analysis, combine the results of these, and graphically present them in an intuitive way, thereby facilitating the analysis of large genomic regions. We''ve decided to call this program Alfresco. We originally wanted to call it Fresco (FRont-End for Sequence COmparison) but that name was already taken. To run Alfresco you need to have jdk1.1 installed. Alfresco has only been tested on Solaris 2.5, Dec OSF 4.0D and Linux, but should run on any machine with jdk1.1. New: Alfresco now runs on Mac and Windows as well.

Proper citation: Alfresco - FRont-End for Sequence COmparison (RRID:SCR_010544) Copy   

•   Source: SciCrunch Registry

http://medicalimaging.wikia.com/wiki/Main_Page

A wiki all about medical imaging. Anyone may contribute who registers. Popular pages include Optical Imaging, Imaging brain function with optical topography, Optical mammography, Introduction to optical imaging, Comparison of time domain and frequency domain systems, Forward problem in diffuse optical imaging, Optical molecular imaging.

Proper citation: Medical Imaging (RRID:SCR_010665) Copy   

•   Source: SciCrunch Registry

http://www.plosone.org/article/info:doi%2F10.1371%2Fjournal.pone.0023501

An algorithm for de novo genome assembly with short paired-end reads.

Proper citation: Meraculous (RRID:SCR_010700) Copy   

•   Source: SciCrunch Registry

http://biomodels.net/miriam/

MIRIAM is an effort to standardise the Minimal Information Required In the Annotation of Models, so that different groups can collaborate on annotating and curating computational models in biology. The goal of the project, initiated by the BioModels.net effort is to produce a set of guidelines suitable for use with any structured format for computational models. MIRIAM is a registered project of the MIBBI (Minimum Information for Biological and Biomedical Investigations). If you are looking for the online resources providing support to MIRIAM Standard, please go to: MIRIAM Resources.

Proper citation: MIRIAM: Minimal Information Required In the Annotation of Models (RRID:SCR_010547) Copy   

•   Source: SciCrunch Registry

http://uberon.org

An integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. The ontology includes comprehensive relationships to taxon-specific anatomical ontologies, allowing integration of functional, phenotype and expression data. Uberon consists of over 10000 classes (March 2014) representing structures that are shared across a variety of metazoans. The majority of these classes are chordate specific, and there is large bias towards model organisms and human.

Proper citation: UBERON (RRID:SCR_010668) Copy   

•   Source: SciCrunch Registry

http://dictybase.org/teaching_tools/index.html

Dictyostelium discoideum is a great organism to use to teach cellular biology. It exhibits very interesting behaviors, such as chemotaxis and phagocytosis, that can readily be studied in standard laboratories without the need for expensive equipment. Lists of labs being used in real courses settings and all necessary information for performing those experiments are provided. Major headings: * Dictyostelium cell biology course, by Dr. David Knecht, University of Connecticut * Dictyostelium cell biology, by Dr. Derrick Brazill, Hunter College, New York * Report on the number of cells in a slug, contributed by John Bonner * Practical on chemotaxis, by Dr. Thierry Soldati, University of Geneva * Comments from Researchers * References suggested by contributors

Proper citation: dictyBase - Teaching Tools Using Dictyostelium discoideum (RRID:SCR_010701) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ubc.ca/matrix2png/

An open visualization tool for the display of matrix data. It is available for download or interactive web use. It is a simple but powerful program for making visualizations of microarray data and many other data types. It generates PNG formatted images from text files of data. It is fast, easy to use, and reasonably flexible. It can be used to generate publication-quality images, or to act as a image generator for web applications. Our group has found it useful for imaging all kinds of matrix-based data, not just microarray data.

Proper citation: Matrix2png (RRID:SCR_010669) Copy   

•   Source: SciCrunch Registry