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http://safcsupplysolutions.com

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A business division of Sigma-Aldrich Corporation, focusing on providing custom manufactured products and specialized services used in the industrial development and manufacturing, including processes, that bring new drugs and new electronic products to market., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SAFC (RRID:SCR_008554) Copy   

•   Source: SciCrunch Registry

http://rocr.bioinf.mpi-sb.mpg.de/

ROCR is a package for evaluating and visualizing the performance of scoring classifiers in the statistical language R. It features over 25 performance measures that can be freely combined to create two-dimensional performance curves. Standard methods for investigating trade-offs between specific performance measures are available within a uniform framework, including receiver operating characteristic (ROC) graphs, precision/recall plots, lift charts and cost curves. ROCR integrates tightly with R''s powerful graphics capabilities, thus allowing for highly adjustable plots. Being equipped with only three commands and reasonable default values for optional parameters, ROCR combines flexibility with ease of usage. Performance measures that ROCR knows: Accuracy, error rate, true positive rate, false positive rate, true negative rate, false negative rate, sensitivity, specificity, recall, positive predictive value, negative predictive value, precision, fallout, miss, phi correlation coefficient, Matthews correlation coefficient, mutual information, chi square statistic, odds ratio, lift value, precision/recall F measure, ROC convex hull, area under the ROC curve, precision/recall break-even point, calibration error, mean cross-entropy, root mean squared error, SAR measure, expected cost, explicit cost. ROCR features: ROC curves, precision/recall plots, lift charts, cost curves, custom curves by freely selecting one performance measure for the x axis and one for the y axis, handling of data from cross-validation or bootstrapping, curve averaging (vertically, horizontally, or by threshold), standard error bars, box plots, curves that are color-coded by cutoff, printing threshold values on the curve, tight integration with Rs plotting facilities (making it easy to adjust plots or to combine multiple plots), fully customizable, easy to use (only 3 commands). ROCR can be used under the terms of the GNU General Public License. Running within R, it is platform-independent.

Proper citation: Classifier Visualization in R (RRID:SCR_008551) Copy   

•   Source: SciCrunch Registry

http://dove.embl-heidelberg.de/Blast2/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. This portal let you search BLAST through the WU-BLAST2 Search Service provided by the Bork Group at EMBL. Sponsors: This resource is supported by EMBL., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bork Group's WU-BLAST2 Search Service at EMBL (RRID:SCR_008431) Copy   

•   Source: SciCrunch Registry

http://cython.org/

Cython is a language that makes writing C extensions for the Python language as easy as Python itself. Cython is based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. The Cython language is very close to the Python language, but Cython additionally supports calling C functions and declaring C types on variables and class attributes. This allows the compiler to generate very efficient C code from Cython code. This makes Cython the ideal language for wrapping external C libraries, and for fast C modules that speed up the execution of Python code. Sponsor. Google and Enthought funded Dag Seljebotn to greatly improve Cython integration with NumPy. Kurt Smith and Danilo Freitas were funded through the Google Summer of Code program to work on improved Fortran and C support respectively.

Proper citation: Cython C-Extensions for Python (RRID:SCR_008466) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/scientific-community/science/programs/cancer/ultrasome

An efficient methodology for detecting and delineating gains and losses of chromosomal material in DNA copy-number data.

Proper citation: Ultrasome (RRID:SCR_008465) Copy   

•   Source: SciCrunch Registry

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   

•   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.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://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   

•   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://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

http://pga.mgh.harvard.edu/oligopicker/

Software to help selecting up to five oligo probes for each of the DNA sequences you provided for microarray spotting.

Proper citation: OligoPicker (RRID:SCR_008720) Copy   

•   Source: SciCrunch Registry

http://www.opentox.org/dev/apis/api-1.1/structure

Tools for the integration of data from various sources (public and confidential), for the generation and validation of computer models for toxic effects, libraries for the development and seamless integration of new algorithms, and scientifically sound validation routines. The goal of OpenTox is to develop an interoperable predictive toxicology framework which may be used as an enabling platform for the creation of predictive toxicology applications. OpenTox is relevent for users from a variety of research areas: Toxicological and chemical experts (e.g. risk assessors, drug designers, researchers) computer model developers and algorithm developers non specialists requiring access to Predictive Toxicology models and data OpenTox applications can combine multiple web services providing users access to distributed toxicological resources including data, computer models, validation and reporting. Applications are based on use cases that satisfy user needs in predictive toxicology. OpenTox was initiated as a collaborative project involving a combination of different enterprise, university and government research groups to design and build the initial OpenTox framework. Additionally numerous organizations with industry, regulatory or expert interests are active in providing guidance and direction. The goal is to expand OpenTox as a community project enabling additional expert and user participants to be involved in developments in as timely a manner as possible. To this end, our mission is to carry out developments in an open and transparent manner from the early days of the project, and to open up discussions and development to the global community at large, who may either participate in developments or provide user perspectives. Cooperation on data standards, data integration, ontologies, integration of algorithm predictions from different methods, and testing and validation all have significant collaboration opportunities and benefits for the community. OpenTox is working to meet the requirements of the REACH legislation using alternative testing methods to contribute to the reduction of animal experiments for toxicity testing. Relevant international authorities (e.g., ECB, ECVAM, US EPA, US FDA) and industry organizations participate actively in the advisory board of the OpenTox project and provide input for the continuing development of requirement definitions and standards for data, knowledge and model exchange. OpenTox actively supports the development and validation of in silico models and algorithms by improving the interoperability between individual systems (common standards for data and model exchange), increasing the reproducibility of in silico models (by providing a quality source of structures, toxicity data and algorithms) and by providing scientifically sound and easy-to-use validation routines. OpenTox is committed to the support and integration of alternative testing methods using in vitro assay approaches, systems biology, stem cell technology, and the mining and analysis of human epidemiological data. Hence the framework design must take into account extensibility to satisfy a broad range of scientific developments and use cases.

Proper citation: OpenTox Framework (RRID:SCR_008686) Copy   

•   Source: SciCrunch Registry

http://www.procure.ca/index.php

The main goal of PROCURE is to provide science and humanity with means to help prevent and cure prostate cancer a disease which this year alone will be diagnosed in an estimated 25,500 Canadian men and one which will, on average, take the lives of 85 men every week. PROCURE strives to redefine the boundaries of research and knowledge by: * Initiating an on-going dialogue with the public and healthcare community to provide needed information and support through accessible means such as: ** A comprehensive website in French and English ** Lectures and special events ** Free book on prostate cancer * Funding and structuring over time a bank of biological materials and data on men with prostate cancer as well as those at risk of developing the disease. Such a Biobank, as it is known, will accelerate breakthrough scientific discovery. Join our alliance today by informing yourself and loved ones. Encourage the other men you care about to have an examination. Make a contribution to our cause. Help us keep information on this site up-to-date. In doing so you will become part of the force against prostate cancer!

Proper citation: PROCURE (RRID:SCR_008722) Copy   

•   Source: SciCrunch Registry

http://dc.crs4.it/projects/biodoop

A suite of parallel bioinformatics applications based upon a popular open-source Java implementation of MapReduce, Hadoop.

Proper citation: Biodoop (RRID:SCR_008711) Copy   

•   Source: SciCrunch Registry

http://www.scioncorp.com/pages/product_prices.htm#Software

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Commercial software vendor.

Proper citation: Scion Image (RRID:SCR_008673) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/drgap/

Designed to identify Driver Genes and Pathways in cancer genome sequencing studies.

Proper citation: DrGaP (RRID:SCR_008670) Copy   

•   Source: SciCrunch Registry

http://www.danga.com/memcached/

A commercial distributed memory object caching system, generic in nature, but originally intended for use in speeding up dynamic web applications by alleviating database load. memcached allows you to take memory from parts of your system where you have more than you need and make it accessible to areas where you have less than you need. With memcached, you can see that all of the servers are looking into the same virtual pool of memory. This means that a given item is always stored and always retrieved from the same location in your entire web cluster.

Proper citation: Memached (RRID:SCR_008625) Copy   

•   Source: SciCrunch Registry

http://www.apache.org/

Provides support for the Apache community of open-source software projects. The Apache projects are characterized by a collaborative, consensus based development process, open and pragmatic software license, and a desire to create high quality software that leads the way in its field.

Proper citation: Apache Software Foundation (RRID:SCR_008588) Copy   

•   Source: SciCrunch Registry