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http://www.sanger.ac.uk/cgi-bin/blast/submitblast/d_rerio

This Blast server offers searches against all D. rerio finished and unfinished clones in the Sanger sequencing pipeline. You can now also search the de novo assemblies generated from sequencing of one doubled haploid homozygous individual of each the AB and Tuebingen strain. Both fish were sequenced to ~40x coverage using Illumina GA sequencing technology and the sequences were assembled using Phusion2, resulting in a 1,33 Gb AB and a 1.48 Gb Tuebingen assembly. Due to the short reads and short inserts and no integration of physical or genetic map data, both assemblies are highly fragmented - with an N50 contig size of about 5kb. Mis-assembly errors may also be present in the contigs. Please note these assemblies are independent additions to the assemblies released by the zebrafish genome project and are intended to aid identification of polymorphisms between these two strains. Charity. Genome Research Limited is a charity registered in England with number 1021457

Proper citation: D. rerio Blast Server (RRID:SCR_008461) Copy   

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http://derisilab.ucsf.edu/

The DeRisi Lab focuses on genomic approaches to the study of infectious disease. Specifically, we are studying Plasmodium falciparum, the causative agent of the most deadly form of human malaria. We are also involved in a major effort for the discovery of new viral pathogens associated with diseases of unknown etiology. Software tools developed in the lab include: HMMSplicer discovers splice sites in high throughput sequencing datasets without using gene models. HMMSplicer can also be used to find non-canonical junctions as well. HMMSplicer was benchmarked on publickly available A. thaliana, H. sapiens, and P. falciparum datasets and performs well on all genomes. Information about the datasets tested, including the exact command parameters and the final results, is provided. HMMSplicer is implemented in Python and is freely available for all. VersaCount is a simple application to assist with the counting of cells by microscopy. When used with a numeric keypad, it can significantly increase counting efficiency when compared with a traditional clicker. Although it was designed for malaria work, it can be customized for a wide variety of cell counting applications. VersaCount was written by Charlie Kim. ExpressionNet is a program written by Jingchun Zhu that uses Bayesian network learning algorithms to explore relationships among random variables to generate network models. The software has been used to study the transcriptional response to environmental perturbations in budding yeast. Details of the program and the study of yeast transcription using Bayesian Networks was published in PLoS ONE. DNA microarrays may be used to identify microbial species present in environmental and clinical samples. However, automated tools for reliable species identification based on observed microarray hybridization patterns are lacking. We present an algorithm, E-Predict, for microarray-based species identification. ArrayOligoSelector (AOS) is an open source program developed by Jingchun Zhu for the purpose of systematically designing gene-specific long oligonucleotide probes for entire genomes. For each open reading frame, the program optimizes oligo selection based upon several parameters, including uniqueness, complexity, secondary structure, GC content, and 3'' end proximity. AOS also is hosted at SourceForge. This site contains documentation and a user-friendly how-to. ArrayMaker 2 provides high performance robotic control of microarrayer robots with an incredibly intuitive, easy to use interface. ArrayMaker 2 is optimized for use with the new generation of ultra fast linear servo driven arrayers, yet it is backwards compatible with the original MGuide style of ball-screw driven arrayers.

Proper citation: DeRisi Lab (RRID:SCR_008581) Copy   

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http://www.rulesbasedmedicine.com/

Rules-Based Medicine (RBM) uses proprietary Multi-Analyte Profiling (MAP) technology to make life science research and drug and diagnostic development programs more efficient and effective. Whether measuring hundreds of biomarkers or simply a few, our approach provides reproducible, quantitative immunoassay data from a small sample volume at a cost-effective price. RBM is CLIA certified and supports GLP studies. * Quality: All immunoassays are validated to clinical laboratory standards. This means complete validation for the clinic, not fit for purpose validation which at RBM means inferior validation. Learn More * Content: We have the most comprehensive menu of biomarker immunoassays available. * Small Sample Volumes: Multiplexing provides you with more data using a smaller sample volume. * Cost Effective: Multiplexing and automation combine to deliver high quality data at reasonable prices. * Ease of use: Ship us your samples and get results within 2 weeks. Rules-Based Medicine (RBM), the worlds leading multiplexed biomarker testing laboratory, provides comprehensive protein biomarker products and services based on its Multi-Analyte Profiling (MAP) technology platform. RBMs biomarker testing service provides pre-clinical and clinical researchers with reproducible, quantitative, multiplexed immunoassay data for hundreds of proteins in a cost-effective manner, from a small sample volume and from multiple species. Our biomarker testing laboratory is CLIA certified and supports GLP studies. Most diseases and drug effects manifest themselves in abnormal levels of specific biomarkers found in the peripheral blood. By providing multiplexed, quantitative, and reproducible tests for hundreds of biomarkers, RBM enables research that historically was not available due to sample volume requirements and associated costs. Use of our testing services can identify the sources of both the positive and negative effects of drugs during pre-clinical research and clinical trials. Biomarker testing results identify patients most likely to respond to a given therapy and the biochemical reason for that response, making clinical trials more successful and effective. Through its wholly owned subsidiary EDI GmbH, RBM provides Human Organo-Typic (HOT) cell culture systems. These co-culture systems consist of multiple primary cell types grown in a 3-D architecture that closely mimic particular human organs and are an ideal platform for ex vivo studies of drug safety and efficacy. RBM combines EDIs cell culture systems with its HumanMAP biomarker testing services to provide researchers with an unprecedented view of the physiological and biochemical impact of a new drug compound or consumer product prior to testing in a human subject. RBM also performs custom assay development, participates in co-sponsored research programs, and pursues in-licensing of novel high-value assays.

Proper citation: Rules Based Medicine (RRID:SCR_008575) Copy   

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http://www.nimblegen.com

Roche NimbleGen, Inc. is a leading innovator, manufacturer and supplier of a proprietary suite of DNA microarrays, consumables, instruments and services. Roche NimbleGen uniquely produces high-density arrays of long oligo probes that provide greater information content and higher data quality necessary for studying the full diversity of genomic and epigenomic variation. Roche NimbleGen is enabling a new era of High-Definition Genomics by providing scientists with cost-effective, high-throughput tools for extracting and integrating complex data on important forms of genomic and epigenomic variation not previously accessible on a genome-wide scale. Scientists can thus obtain a clearer understanding of genomic and epigenomic structure and function and how they impact biology and medicine. This improved performance is made possible by Roche NimbleGen''s proprietary Maskless Array Synthesis (MAS) technology, which uses digital light processing and rapid, high-yield photochemistry to synthesize long oligo, high-density DNA microarrays with extreme flexibility. NimbleGen Systems was established in 1999. The MAS technology is the result of research collaborations between the departments of biotechnology, genetics, physics, and semiconductor engineering at the University of Wisconsin - Madison. Roche NimbleGen has the exclusive worldwide license to the MAS technology from the Wisconsin Alumni Research Foundation (WARF).

Proper citation: Roche NimbleGen (RRID:SCR_008571) Copy   

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http://www.neuroscience.cam.ac.uk/

This portal provides information about the neuroscience department at the University of Cambridge. Cambridge has a strong tradition in neuroscience having been host to the first analyses of neural signaling in the 1930s, determined the mechanisms of neuronal firing in the 1950s, and heralded some of the early theoretical approaches to the functions of neural circuitry in the 1960s. Neuroscience continues to grow at Cambridge, with an impressive record of achievement in multidisciplinary research.

Proper citation: Cambridge Neuroscience Department (RRID:SCR_008649) Copy   

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http://www.neurosciencenetwork.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An initiative to build connections among the many powerful resources across the region. Between colleges and universities, pharmaceutical and biotechnology companies, device developers, startups and service businesses, the Cure Corridor, Einsteins''s Alley, the Pharm Belt, or whatever you like to call the region, offers opportunities for discovery and development of new therapies that is unmatched. Sponsors: The NeuroScience Network is made possible, in part, through funding from Bio 1 WIRED.

Proper citation: The NeuroScience Network (RRID:SCR_008648) Copy   

•   Source: SciCrunch Registry

http://www.transgenic-hydra.org/

The Transgenic Hydra Facility is a non-profit facility in the laboratory of Thomas Bosch at the University of Kiel that assists scientists to use and to develop transgenic Hydra polyps. Our mission is to provide investigators access to the latest technology for the efficient production of transgenic polyps. We particularly encourage scientists from laboratories lacking the infrastructure for transgenic Hydra technologies to use our services. Abstract: Understanding the evolution of development in large part relies on the study of phylogenetically old organisms. Cnidarians, such as Hydra, have become attractive model organisms for these studies. However, despite long-term efforts, stably transgenic animals could not be generated, severely limiting the functional analysis of genes. Here we report the efficient generation of transgenic Hydra lines by embryo microinjection. One of these transgenic lines expressing EGFP revealed remarkably high motility of individual endodermal epithelial cells during morphogenesis. We expect that transgenic Hydra will become important tools to dissect the molecular mechanisms of development at the base of the Metazoan tree. Sponsors: Financial support for this research was provided by the German Research Foundation [Deutsche Forschungsgemeinschaft Grants B0848/13 and SFB617.

Proper citation: Transgenic Hydra Facility (RRID:SCR_008641) Copy   

•   Source: SciCrunch Registry

http://developer.yahoo.com/yui/

The YUI Library is a set of utilities and controls, written with JavaScript and CSS, for building richly interactive web applications using techniques such as DOM scripting, DHTML and AJAX. YUI is available under a BSD license and is free for all uses. YUI is proven, scalable, fast, and robust. Built by frontend engineers at Yahoo! and contributors from around the world, it''s an industrial-strength JavaScript library for professionals who love JavaScript.

Proper citation: Yahoo Developer Network (RRID:SCR_008594) Copy   

•   Source: SciCrunch Registry

http://www.aquatichabitats.com

Aquatic Habitats (AHAB) is the worlds largest manufacturer of housing systems for aquatic research animals. We are biologists first and engineers second, so we understand the complexity of aquatic life and how to sustain it. Our turnkey systems are secure, efficient and as fail-safe as possible.

Proper citation: Aquatic Habitats (RRID:SCR_008597) Copy   

•   Source: SciCrunch Registry

http://www.ltp-program.com

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Jan 16th 2025. WinLTP is a stimulation, data acquisition and on-line analysis electrophysiological software for studying Long-Term Potentiation (LTP), Long-term Depression (LTD), and related phenomena. WinLTP is multitasking and simultaneously runs 1) LTP stimulus/acquisition/analyzing sweeps with protocol scripting, and 2) continuous acquisition saving Axon Binary Files (abf). WinLTP runs on Windows PCI bus computers and uses National Instruments PCI M-Series boards and Axon Instruments'' Digidata 1320A and 1322A data acquisition boards. Other software that can use the M-Series boards includes Axograph Scientific''s AxoGraph X, WaveMetrics'' IGOR, National Instruments'' LabView, John Dempster''s Strathclyde Electrophysiology Suite (WinWCP and WinEDR), Silver lab''s Nclamp, and QUB data acquisition., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: WinLTP (RRID:SCR_008590) Copy   

•   Source: SciCrunch Registry

http://motif-x.med.harvard.edu

motif-x (short for motif extractor) is a software tool designed to extract overrepresented patterns from any sequence data set. The algorithm is an iterative strategy which builds successive motifs through comparison to a dynamic statistical background.

Proper citation: Motif Extractor (RRID:SCR_008628) Copy   

•   Source: SciCrunch Registry

http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:DelPhi

DelPhi provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution. The current version is fast, accurate, and can handle extremely high lattice dimensions. It also includes flexible features for assigning different dielectric constants to different regions of space and treating systems containing mixed salt solutions. DelPhi takes as input a coordinate file format of a molecule or equivalent data for geometrical objects and/or charge distributions and calculates the electrostatic potential in and around the system, using a finite difference solution to the Poisson-Boltzmann equation. DelPhi is a versatile electrostatics simulation program that can be used to investigate electrostatic fields in a variety of molecular systems. Features of DelPhi include solutions to mixtures of salts of different valence; solutions to different dielectric constants to different regions of space; and estimation of the best relaxation parameter at run time.

Proper citation: DelPhi (RRID:SCR_008669) Copy   

•   Source: SciCrunch Registry

http://www.de-idata.com

A commercial organization that suppplies software which creates separate HIPAA-compliant repositories of de-identified patient records and reports. This software allows clinicians, researchers, and administrative leadership to safely access, search, share, and analyze de-identified patient-level data. DE-ID can be acquired as stand-alone tool or integrated with data networks or clinical information systems.

Proper citation: DE-ID Data Corp (RRID:SCR_008668) Copy   

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http://www.bic.mni.mcgill.ca/users/crisco/jiv/

JIV is a Java software for visualization and side-by-side comparison of multiple 3D image datasets. While it was originally designed for remote data access, it can be used as a traditional local application as well. It features include being highly portable and platform-independent, the ability to run with a common Web browser and to cope with slow network links, an independent 3D image data format, and a display of gray-level (intensity) image data with a user-controlled color-mapping, among other features.

Proper citation: JIV: A 3D Image Data Visualization and Comparison Tool (RRID:SCR_008657) Copy   

•   Source: SciCrunch Registry

http://www.oracle.com/us/sun/index.htm

Oracle''s complete, open, and integrated product strategy provides flexibility and choice to our customers across their IT infrastructure. Now, with Sun server, storage, operating-system, and virtualization technology, Oracle is the only vendor able to offer a complete technology stack in which every layer is integrated to work together as a single system. Oracle''s open architecture and multiple operating-system options gives our customers unmatched benefits, including excellent system availability, scalability, energy efficiency, powerful performance, and low total cost of ownership Starting more than 30 years ago with Oracle''s innovative relational database, the Oracle stack today includes Oracle Enterprise Linux, Oracle VM, Oracle Fusion Middleware, and the largest and most complete set of industry and business applications software on the market. The addition of Sun storage and systems technology makes the Oracle stack complete. Oracle integrates every layer of the IT stack to deliver compelling value, based on high system availability and security, stunning performance, and low TCO. Only Oracle can offer this stack advantage to its customers through deep and seamless integration between the tiers that our competitors cannot match.

Proper citation: SUN Interface Engine (RRID:SCR_008659) Copy   

•   Source: SciCrunch Registry

http://portal.ncibi.org/gateway/bcde.html

Biological Concept Diagram Editor (BCDE) is a conceptual relationship diagramming tool specifically designed for biomedical researchers. It allows for efficient knowledge and data capture, fast diagram creation, easy data retrieval, and flexible exporting. The BCDE application is the main diagramming tool in the system. Through it, users can create, modify, load, and save BCDE diagrams. The diagrams created with BCDE application are network oriented. Each BCDE figure can be annotated using fields from the BioPAX level II format. In addition, a user can add URL links and attachments to a BCDE figure. Diagrams generated in BCDE are stored in the BCDE XML format for better database integration and better data extraction.

Proper citation: Biological Concept Diagram Editor (RRID:SCR_008654) Copy   

•   Source: SciCrunch Registry

http://www.sciencebuddies.org

Many science fairs have a group of people called a Scientific Review Committee (or SRC) that reviews each project application to ensure that all safety and legal requirements will be met and that the appropriate forms have been completed. The committee also reviews the completed project displays. Typically, a Scientific Review Committee is composed of at least three people: a biomedical scientist, a physical scientist, and a science teacher. Some fairs also have an Institutional Review Board (IRB), which reviews all proposed projects that in any way involve human beings. An IRB''s purpose is to ensure that the project will not present undue risk to the subjects.

Proper citation: Scientific Review Committee (RRID:SCR_008652) Copy   

•   Source: SciCrunch Registry

https://www.stat.auckland.ac.nz/~paul/plaudits/Iobion.htm

GeneTraffic is a web-based microarray data analysis and management software developed by Iobion Informatics that allows users to log onto a server, upload their microarray data and perform analysis and project management remotely. GeneTraffic was made by Iobion Informatics (now under Stratagene) and can be accessed thorough Internet Explorer 6.0 or greater on Windows XP.

Proper citation: GeneTraffic (RRID:SCR_008651) Copy   

•   Source: SciCrunch Registry

http://www.usc.edu/schools/medicine/departments/psychiatry_behavioralsciences/research/gsc/

The USC Geriatric Studies Center includes the State of California Alzheimer's Research Center of California and the National Institute of Aging funded clinical program of the USC Alzheimer's Disease Research Center. It is staffed by USC faculty and physicians with expertise in Alzheimer's disease and age related memory loss. The Center provides evaluation, diagnosis and treatment recommendations, referral to caregiver services and support groups, and the opportunity to participate in clinical drug trials for memory problems.

Proper citation: USC Geriatric Studies Center/Alzheimer's Disease Research Center (RRID:SCR_008725) Copy   

•   Source: SciCrunch Registry

http://human-phenotype-ontology.github.io/

The Disease Ontology group has developed a set of standard representations of phenotypes associated with diseases useful in bioinformatics applications. These are formalized into an ontological structure and are encoded in OWL. Neurodegenerative diseases have a wide and complex range of biological and clinical symptoms. While neurodegenerative diseases share many pathological features in common, they also contain unique signatures. Animal models of these disorders are key to translational research. However, animal models typically replicate only a subset of disease features or display features that are only indirectly related to a given disorder, whose relationship to the human condition may be across several diseases. Matching animal models to human diseases is therefore a significant informatics challenge. We have been working to develop ontologies that capture essential features of neurodegenerative diseases and associated animal models in a way that allows more flexible matching of animal models to human disorders and in a way that makes explicit commonalities and differences among animal models and human neurodegenerative disease. Creating ontologies for diseases and disorders is a very challenging task (Gupta et al., 2003) because of the complexity of the disorders and because of the limitations of current ontology formalisms. In order to simplify the approach and make it practical for use in information systems, we have focused on formal descriptions of phenotypes associated with diseases and animal models rather than on a formal model of the disease process itself. We employ the modular ontologies developed as part of the Neuroscience Information Framework (NIF: http://nif.nih.gov) and the Phenotype and Trait Ontology (PATO), an ontology of qualities associated with biological phenotypes, to create a flexible template for creating phenotypic statements at the class and instance levels. We show how these phenotypes can be used to look for commonalities across multiple neurodegenerative conditions and animal models.

Proper citation: Disease Phenotype Ontology (RRID:SCR_008687) Copy   

•   Source: SciCrunch Registry