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http://www.xiphophorus.txstate.edu/

Supplier of xiphophorus (platyfish or swordtails) from pedigreed parental lines, representing variety of species. In addition to supplying strains and providing consultation on husbandry and genetic questions, the XGSC produces custom interspecies hybrids (both first generation F1, and backcross hybrid generation BC1) for a variety of projects.

Proper citation: Xiphophorus Genetic Stock Center (RRID:SCR_008340) Copy   

•   Source: SciCrunch Registry

http://www.med.nus.edu.sg/ant/histonet/txt/menu/nervmenu.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 18, 2013. 15 annotated electron micrographs of different parts of the nervous system. Different nerve tissues are depicted.

Proper citation: Nerve Tissue (RRID:SCR_008219) Copy   

•   Source: SciCrunch Registry

http://www.nature.com/nature/supplements/collections/

This website provides summary collections written for a broad audience highlighting some of the significant advances in a particular field. These are not scientific articles although they may reference scientific work. Sponsors: This resource is supported by Nature.com

Proper citation: Nature Supplements: Collections archive (RRID:SCR_008337) Copy   

•   Source: SciCrunch Registry

http://www.ini.uzh.ch/

The mission of the Institute is to discover the key principles by which brains work and to implement these in artificial systems that interact intelligently with the real world. The Institute of Neuroinformatics is built of many people covering a wide range of disciplines and research areas. The major research projects and areas are listed below. - Behavior and Cognition: At the Institute of Neuroinformatics researchers investigate in Behavior and Cognition on various levels, ranging from neuronal circuit models of learning and adaptation over psychophysical experiments for color constancy up to modeling complex behavioral tasks such as exploration and goal-directed navigation. - Computation in Neural Circuits: By examining the brains of cats, rats and monkeys, and by making simulations of the cortex, INI hopes to learn how this circuit performs such widely different tasks. This knowledge might lead to advances in how computers are designed, and will certainly lead to advances in the subtlety and power of medical neuroscience. - Neurotechnologies: INI aims to harness the principles of biological computation, which can be expected to have a major impact on the technology market as autonomous intelligence pervades equipment, vehicles, buildings, utilities and clothing. Sponsors: INI is supported by European Union (EU), Gerbert Ruf Stiftung, Neuroscience Center (ZNZ), Swiss Confederation (KTI), Swiss Federal Institute of Technology Zurich (ETH), Swiss National Science Foundation (SNF), University of Zurich (UZH), and VW Stiftung

Proper citation: Institute of Neuroinformatics (RRID:SCR_008331) Copy   

•   Source: SciCrunch Registry

http://www.snprc.org/

Center that supports studies of nonhuman primate models of human diseases, including common chronic diseases and infectious diseases and the effects that genetics and the environment have on physiological processes and disease susceptibility. SNPRC encourages the use of its resources by investigators from the national and international biomedical research communities.

Proper citation: Southwest National Primate Research Center (RRID:SCR_008292) Copy   

•   Source: SciCrunch Registry

http://www.uhnres.utoronto.ca/facilities/wcif/download.php

The ImageJ installations below correspond to the WCIF ImageJ manual. The manual is written for this particular installation of ImageJ. This ImageJ installation has, among other plugins, one that links to an online version of the manual. The online manual is more up-to-date than the PDF version. Windows users Download WCIF ImageJ bundle (~23Mb) v1.34i, 3rd March 2005 with J2SE 5.0 (formerly J2SE 1.5). For Windows: download and run program. Mac and Linux users Download your OS specific version of ImageJ from the ImageJ website then extract the following file to the plugins folder. Download WCIF ImageJ bundle plugins only (~2Mb) This contains only the plugins, IJ preferences, LUTs and plugin source code. Image Processing and Analysis Software ImageJ LSM Browser (*.lsm) Axiovision viewer (*.zvi) Manufacturers of our microscopes and related equipment Zeiss - Microscopes and imaging systems. P.A.L.M. Microlaser Technologies - Manufacturer of our laser capture system. Sutter Instruments - Micromanipulators. Uniblitz - Shutters. Ludl - Manufacturers of our motorised x-, y-stage Hamamatsu - Digital cameras. Molecular Probes - Dyes and reagents. Scanalytics - Image acquisition and processing software. MicroBrightField - Developers of the Neurolucida and Stereo Investigator software. DVC - Digital cameras. Bitplane - Developers of the Imaris suite of software. AutoQuant - Developers of the AutoDeblur deconvolution software

Proper citation: Wright Cell Imaging Facility (RRID:SCR_008488) Copy   

•   Source: SciCrunch Registry

http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html

A prediction algorithm based on the helix/coil transition theory. Agadir predicts the helical behaviour of monomeric peptides. It only considers short range interactions. Conditions such as pH, temperature and ionic strength are used in the calculation. Modifications of the termini are also allowed. To submit a job to Agadir, log in the calculation part using the login button in the right bottom. Then fill-in the input form and proceed to next page, etc. You will reach a final page that resumes all the input information and allows you to run the calculation. You can submit one or more peptide sequences in one-letter format. Sequences should be separated by one return character. Spaces and tabulations are automatically removed. Only standard amino acids are accepted. Agadir accepts two modifications at the N-terminus (acetylation or succynilation), and one at the C-terminus (amidation). Just choose the desired option in the input form. You can use only one set of parameters: temperature, ionic strength (calibrated for NaCl) and pH, or explore a particular range of conditions for one parameter. In the latter case the intervals between any two values are: Ionic strength 0.05 M Temperature 1 K pH 0.2 units When setting the conditions for these parameters please be aware that the allowed ranges are: Ionic strength between 0.001 and 1 M Temperature between 273 and 400 K pH between 1 and 14 Output of the prediction at the residue level is available only when submitting no more than ten peptide sequences, and without any screening of conditions. Hstaple is the Hydrophobic Staple motif, Schellman is the Shellman motif, CaH are the expecte chemical shifts of the Calpha proton, 13Ca are the alpha Carbon 13 chemical shifts, JaN is the Jalpha--nitrogen coupling.

Proper citation: Agadir (RRID:SCR_008402) Copy   

•   Source: SciCrunch Registry

http://www.epidata.dk

Sustainability plan EpiData Software has since 2000 grown from securing the principles of Epi Info V6 to an independent and documentation based system with several translations and numerous downloads. To secure continued viability organisations and governments work is being done to secure for the future, see also the license principles - the ambition is to convert the programs to open-source within few years. Contributions are used for costs of development after version 1.5 (e.g. refining of programming, enhancing speed, maintenance of website, to pay for absence from paid work to do EpiData or other developmental and promotional efforts for EpiData). About the EpiData Association EpiData Software is from EpiData Entry version 2.0 and above released by the non-profit organisation The EpiData Association Odense, Denmark (In Danish: EpiData foreningen). The association receives NO baseline budget from anyone. The association has no employees Postal adress is: The EpiData Association, att. Jens Lauritsen, Enghavevej 34, DK5230 Odense M, Denmark, Europe The body of users of EpiData form the most important part of the basis of the EpiData Association. Those who choose to register as users will be asked when desicions are to made regarding additions to the program. Needs for documentation etc. Registration is done by adding your e-mail to the Information list. Supporting members or institutions adds to the foundation and development of EpiData by securing funding to pay for the associated costs. List of donors. The board of the association is made up of the core persons developing EpiData, currently Jens M.Lauritsen and Michael Bruus in collaboration with experienced users and the Friends Of EpiData group (FoED), comprising a group of international persons wishing to support the development of EpiData Sponsor. Without support from a number of NGO''s, Universities, Regional Health Authorities and other funding bodies EpiData development would have stopped

Proper citation: EpiData Software (RRID:SCR_008485) Copy   

•   Source: SciCrunch Registry

http://www.theseed.org/DinsdaleSupplementalMaterial/

his table shows the metadata and links to sources of the data and citations associated with the publicly available metagenome sequences used in the Dinsdale, Edwards, et al., analysis of 87 different metagenomes. The links will take you to the annotated sequences in the metagenomics SEED, CAMERA, and the NCBI Short Read Archve. Please note that all metagenomes are currently available to download via the ftp links, some are available in the meta-RAST, and other links will be added as soon as they become available. Citations for individual metagenomes will also be added as and when they become available. DNA sequences for all metagenomes are avaialble via anonymous FTP. Sponsor. This project was supported by the Gordon and Betty Moore Foundation Marine Microbial Initiative, National Science Foundation grants (F.R. and D.L.V.), a Department of Commerce ATP grant (F.R.), a National Research Initiative Competitive Grant from the USDA Cooperative State Research, Education and Extension Service (B.W.), the National Institute of Allergy and Infectious Diseases, the National Institutes of Health and the Department of Health and Human Services (R.S.).

Proper citation: Metagenomes Used in The Statistical Analysis (RRID:SCR_008483) Copy   

•   Source: SciCrunch Registry

http://www.dialog.com

Dialog provides critical information from the world''s most authoritative publishers, combined with the tools to search every bit of it with speed and precision. With direct operations in 27 countries, Dialog products and services are a combination of highly accurate online research tools offering access to unique and relevant databases designed to meet the specific needs of a wide range of users. Information professionals and end-users at business, professional, scientific, academic and government organizations in more than 100 countries prize Dialog services to meet their searching needs. As part of the Deep Web, which is estimated to be 500 times larger than the content accessible via Web search engines, Dialog products offer unparalleled depth and breadth of content coupled with the ability to search with precision and speed. Our collection of over 900 databases handles more than 700,000 searches and delivers over 17 million document page views per month. Searchable content on Dialog services includes articles and reports from thousands of real-time news feeds, newspapers, broadcast transcripts and trade publications, plus market research reports and analyst notes providing support for financial decision-making, as well as in-depth repositories of scientific and technical data, patents, trademarks and other intellectual property data. Additional content areas include government regulations, social sciences, food and agriculture, reference, energy and environment, chemicals, pharmaceuticals and medicine.

Proper citation: Dialog (RRID:SCR_008482) Copy   

•   Source: SciCrunch Registry

http://www.flintbox.com/technology.asp?page=3716

Welcome to Flintbox, an application that revolutionizes the way the innovation community can share technologies, distribute new materials and software, and collaborate on research projects. Hundreds of research institutions are participating in the Flintbox open innovation network. Become a member to contribute and explore We are excited to present the Flintbox Application Programming Interface (API) to provide users with an easy way to upload data from any system to Flintbox. This freely available tool for synchronized information exchange will be a valuable resource to the open innovation community. The Flintbox API gives you the power to: Import existing technology postings directly into Flintbox Avoid duplicate data entry to market your technologies, ideas, and materials Create postings from any database Export project information to other websites For more information about using and implementing the Flintbox API, please see the About the Flintbox API page. Featured Project The New Flintbox offers expanded transactional capabilities: credit cards, purchase orders, purchase authorizations, donations, and much more The global Flintbox community is ideal for marketing new technologies, creative works, course materials, and innovative ideas. Flintbox enables universities to maximize their outreach to a broad spectrum of the innovation community. Plus, Wellspring provides expertise in assisting TTOs, inventors, and industrial liaison offices to promote their technologies, research programs, and partnering opportunities to Flintbox. Flintbox for Corporations Corporations turn to Flintbox to cultivate existing relationships and engage in new opportunities for collaborative research and solution sourcing from universities and other companies. For example, a pharmaceutical firm uses Flintbox to provide researchers and physicians software to assess patient outcomes. Flintbox for Technology Communities Flintbox empowers technology communities to connect effectively in a geographic region, building a Sphere of Innovation to truly recognize and capitalize on the valuable relationships and innovation assets in your community. For example, by creating or joining a community Group of members with common interests, say tissue engineering or artificial intelligence, you can link to other groups and explore common interests and complementary resources, for a dynamic collaborative effort and to efficiently share related technology projects. Flintbox is a registered trademark of Wellspring Worldwide, LLC

Proper citation: Flintbox (RRID:SCR_008519) Copy   

•   Source: SciCrunch Registry

http://tree.bio.ed.ac.uk/software/figtree

A graphical viewer of phylogenetic trees and a program for producing publication-ready figures. It is designed to display summarized and annotated trees produced by BEAST.

Proper citation: FigTree (RRID:SCR_008515) Copy   

•   Source: SciCrunch Registry

http://www.fltk.org

This document defines the processes and standards that all FLTK developers must follow when developing and documenting FLTK, and how trouble reports are handled and releases are generated. The purpose of defining formal processes and standards is to organize and focus our development efforts, ensure that all developers communicate and develop software with a common vocabulary/style, and make it possible for us to generate and release a high-quality GUI toolkit which can be used with a high degree of confidence. Much of this file describes the existing practices that have been used up through FLTK 1.1.x, however I have also added some new processes/standards to use for future code and releases. The fltk-dev mailing list and fltk.development newsgroup are the primary means of communication between developers. All major design changes must be discussed prior to implementation. Specific Goals The specific goals of the FLTK are as follows: Develop a C++ GUI toolkit based upon sound object-oriented design principles and experience. (*) Minimize CPU usage (fast). (*) Minimize memory usage (light). (*) Support multiple operating systems and windowing environments, including UNIX/Linux, MacOS X, Microsoft Windows, and X11, using the native graphics interfaces. (*) Support OpenGL rendering in environments that provide it. (*) Provide a graphical development environment for designing GUI interfaces, classes, and simple programs. (*) Support UTF-8 text. Support printer rendering in environments that provide it. Support schemes, styles, themes, skinning, etc. to alter the appearance of widgets in the toolkit easily and efficiently. The purpose is to allow applications to tailor their appearance to the underlying OS or based upon personal/user preferences. Support newer C++ language features, such as templating via the Standard Template Library (STL), and certain Standard C++ library interfaces, such as streams. However, FLTK will not depend upon such features and interfaces to minimize portability issues. Support intelligent layout of widgets. Many of these goals are satisfied by FLTK 1.1.x (*), and many complex applications have been written using FLTK on a wide range of platforms and devices. Development of the remaining features is proceding for FLTK 2.0 with a new, namespace-based API. While 2.0 offers some limited 1.x source compatibility, the changes to the underlying widget classes are significant enough to prevent full compatibility. Software Development Practices Documentation All widgets are documented using the Doxygen software; Doxygen comments are placed in the header file for the class comments and any inline methods, while non-inline methods should have their comments placed in the corresponding source file. The purpose of this separation is to place the comments near the implementation to reduce the possibility of the documentation getting out of sync with the code. All widgets must have a corresponding test program which exercises all widget functionality and can be used to generate image(s) for the documentation. Complex widgets must have a written tutorial, either as full text or an outline for later publication The final manuals are formatted using the HTMLDOC software. Sponsor. Easy Software Products

Proper citation: Fast Light Toolkit (RRID:SCR_008514) Copy   

•   Source: SciCrunch Registry

http://fluxus-technology.com/sharenet.htm

DNA software and consultancy: The DNA Alignment software and Network software is used by biologists, anthropologists, medical researchers and students world wide. We carry out phylogeographic consultancy for US, UK and German clients, including legal medical work. We were involved in the tv projects The Real Eve (Discovery Channel) and Motherland (BBC). Our biotechnological director Dr Peter Forster is on the editorial board of the International Journal of Legal Medicine since 1999. Technology and sales consultancy: Clients include multinational corporations, research institutions, and medium to small businesses. Client quotes: Vorbildlicher Einsatz (Dr Stephan Hitzel, EADS, in CADplus 1/2003 journal, Cover Story). We have had an effective business relationship with Fluxus Technology since 1999, and their experience of the German market has proved to be invaluable as part of our operations supplying high end engineering software and consultancy services right across the engineering supply chain (Andy Chinn, Business Development Manager, ITI TranscenData, February 2006). Abstract. Indo-European is the largest and best-documented language family in the world, yet the reconstruction of the Indo-European tree, first proposed in 1863, has remained controversial. Complications may include ascertainment bias when choosing the linguistic data, and disregard for the wave model of 1872 when attempting to reconstruct the tree. Essentially analogous problems were solved in evolutionary genetics by DNA sequencing and phylogenetic network methods, respectively. We now adapt these tools to linguistics, and analyze Indo-European language data, focusing on Celtic and in particular on the ancient Celtic language of Gaul (modern France), by using bilingual GaulishLatin inscriptions. Our phylogenetic network reveals an early split of Celtic within Indo-European. Interestingly, the next branching event separates Gaulish (Continental Celtic) from the British (Insular Celtic) languages, with Insular Celtic subsequently splitting into Brythonic (Welsh, Breton) and Goidelic (Irish and Scottish Gaelic). Taken together, the network thus suggests that the Celtic language arrived in the British Isles as a single wave (and then differentiated locally), rather than in the traditional two-wave scenario (P-Celtic to Britain and Q-Celtic to Ireland). The phylogenetic network furthermore permits the estimation of time in analogy to genetics, and we obtain tentative dates for Indo-European at 8100 BC 1,900 years, and for the arrival of Celtic in Britain at 3200 BC 1,500 years. The phylogenetic method is easily executed by hand and promises to be an informative approach for many problems in historical linguistics.

Proper citation: Fluxus (RRID:SCR_008517) Copy   

•   Source: SciCrunch Registry

http://www.daylight.com/dayhtml/doc/theory/

Daylight provides enterprise-level cheminformatics software technologies to life science companies. Our superior chemistry, high performance, and open architecture have earned Daylight a reputation for delivering the state-of-the-art in chemical information processing since 1987. Daylight Chemical Information Systems, Inc. is a privately held company with corporate offices in Aliso Viejo, CA and research offices in Santa Fe, NM and Cambridge, England. Support At Daylight, support means a wide array of services that are designed to empower users to make the most of Daylight software. We offer detailed administration documentation and guides through this website. Our User Group Meetings allow in-depth exploration of our technology. And, of course, our support staff is available to assist you whenever the need occurs. Download - Downloading current releases as well as contributed code, system requirements, installation directions, and release information Reference Guides - List of available documentation such as programming guides and user manuals. Cheminformatics - List of additional general resources including introductory materials, theory manual, tutorials and user meeting archives. Sponsor. Daylight

Proper citation: Daylight (RRID:SCR_008474) Copy   

•   Source: SciCrunch Registry

http://helixweb.nih.gov/dnaworks

DNAWorks automates the design of oligonucleotides for gene synthesis by PCR-based methods. The availability of sequences of entire genomes has dramatically increased the number of protein targets, many of which will need to be overexpressed in cells other than the original source of DNA. Gene synthesis often provides a fast and economically efficient approach. The synthetic gene can be optimized for expression and constructed for easy mutational manipulation without regard to the parent genome. DNAWorks accesses a computer program that automates the design of oligonucleotides for gene synthesis. The website provides forms for simple input information, i.e. amino acid sequence of the target protein and melting temperature (needed for the gene assembly) of synthetic oligonucleotides. The program outputs a series of oligonucleotide sequences with codons optimized for expression in an organism of choice. Those oligonucleotides are characterized by highly homogeneous melting temperatures and a minimized tendency for hairpin formation. The approach presented here simplifies the production of proteins from a wide variety of organisms for genomics-based studies.

Proper citation: DNAWorks at Helix Systems (RRID:SCR_008470) Copy   

•   Source: SciCrunch Registry

http://www.ebtox.org

This website is an invitation. an invitation to join scientists and stakeholders in an effort to review the scientific basis of traditional toxicological risk assessment, to provide the toxicological community with the tools it needs to efficiently and transparently judge risks of a diversifying nature and to make toxicology thus fit to meet the challenges of the 21st century. an invitation to participate in the inception and continuous implementation of a new movement in toxicology that aims at adopting an evidence-based approach. an invitation to help bridging the gap between modern toxicological science and risk assessment in order to exploit the wealth of information from new technologies in modern life sciences & toxicological research and to arrive at informed, transparent, judicious and conscientious decisions made on the basis of all evidence available. an invitation to develop a framework that allows combining precious expert insight grown over years of practical experience with structured approaches in basic science, in method assessment and in decision-making. Such evidence-based toxicology might help to make the best possible use of all sources of evidence in an efficient, productive, reliable, acceptable and transparent manner. Why do we need evidence-based toxicology (EBT)? Toxicology and the delivery of effective safety assessment critically relies on concepts and understanding generated by basic scientific research and must therefore adapt constantly to advances in knowledge. However, particularly from the perspective of regulatory toxicology, some of the assessment paradigms and methodologies were established decades ago and have changed little in response to scientific progress. At the same time, changes in our understanding of human disease, changes in the types of product now requiring safety assessment, and changes in the legislative landscape and public expectations pose significant challenges for industry, academia and regulators alike. It is necessary to challenge the status quo and ensure that as a matter of course best scientific practice and technical sophistication is reflected in safety assessment practices such that current and future challenges can be met. It is important therefore to ensure that structures are available that will encourage, facilitate and support a process of critical appraisal and renewal of the toxicological repertoire available for safety assessment. Part of this process is to embrace evidence-based toxicology such that the best possible scientific evidence is applied to judge product safety and likely risks to human health.

Proper citation: Evidence Based Toxicology (RRID:SCR_008507) Copy   

•   Source: SciCrunch Registry

http://www.biodas.org

The Distributed Annotation System (DAS) defines a communication protocol used to exchange annotations on genomic or protein sequences. It is motivated by the idea that such annotations should not be provided by single centralized databases, but should instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is done by DAS clients. The advantages of this system are that control over the data is retained by data providers, data is freed from the constraints of specific organisations and the normal issues of release cycles, API updates and data duplication are avoided. DAS is a client-server system in which a single client integrates information from multiple servers. It allows a single machine to gather up sequence annotation information from multiple distant web sites, collate the information, and display it to the user in a single view. Little coordination is needed among the various information providers. DAS is heavily used in the genome bioinformatics community. Over the last years we have also seen growing acceptance in the protein sequence and structure communities. A DAS-enabled website or application can aggregate complex and high-volume data from external providers in an efficient manner. For the biologist, this means the ability to plug in the latest data, possibly including a user''s own data. For the application developer, this means protection from data format changes and the ability to add new data with minimal development cost. Here are some examples of DAS-enabled applications or websites for end users: :- Dalliance Experimental Web/Javascript based Genome Viewer :- IGV Integrative Genome Viewer java based browser for many genomes :- Ensembl uses DAS to pull in genomic, gene and protein annotations. It also provides data via DAS. :- Gbrowse is a generic genome browser, and is both a consumer and provider of DAS. :- IGB is a desktop application for viewing genomic data. :- SPICE is an application for projecting protein annotations onto 3D structures. :- Dasty2 is a web-based viewer for protein annotations :- Jalview is a multiple alignment editor. :- PeppeR is a graphical viewer for 3D electron microscopy data. :- DASMI is an integration portal for protein interaction data. :- DASher is a Java-based viewer for protein annotations. :- EpiC presents structure-function summaries for antibody design. :- STRAP is a STRucture-based sequence Alignment Program. Hundreds of DAS servers are currently running worldwide, including those provided by the European Bioinformatics Institute, Ensembl, the Sanger Institute, UCSC, WormBase, FlyBase, TIGR, and UniProt. For a listing of all available DAS sources please visit the DasRegistry. Sponsors: The initial ideas for DAS were developed in conversations with LaDeana Hillier of the Washington University Genome Sequencing Center.

Proper citation: Distributed Annotation System (RRID:SCR_008427) Copy   

•   Source: SciCrunch Registry

http://seqpig.sourceforge.net/

A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters.

Proper citation: SeqPig (RRID:SCR_008548) Copy   

•   Source: SciCrunch Registry

http://biosig.sourceforge.net/

Software library for processing of electroencephalogram (EEG) and other biomedical signals like electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), respiration, and so on. Biosig contains tools for quality control, artifact processing, time series analysis, feature extraction, classification and machine learning, and tools for statistical analysis. Many tools are able to handle data with missing values (statistics, time series analysis, machine learning). Another feature is that more then 40 different data formats are supported, and a number of converters for EEG,, ECG and polysomnography are provided. Biosig has been widely used for scientific research on EEG-based BraiN-Computer Interfaces (BCI), sleep research, and ECG and HRV analysis. It provides software interfaces several programming languages (C, C++, Matlab/Octave, Python), and it provides also an interactive viewing and scoring software for adding, and editing of annotations, markers and events.

Proper citation: BioSig: An Imaging Bioinformatics System for Phenotypic Analysis (RRID:SCR_008428) Copy   

•   Source: SciCrunch Registry