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http://vortex.cs.wayne.edu/projects.htm#Onto-Miner

Onto-Miner (OM) provides a single and convenient interface that allows the user to interrogate our databases regarding annotations of known genes. OM will return all known information about a given list of genes. Advantages of OM include the fact it allows queries with multiple genes and allows for scripting. This is unlike GenBank which uses a single gene navigation process. Scripted search of the Onto-Tools database for gene annotations. User account required. Platform: Online tool

Proper citation: Onto-Miner (RRID:SCR_005722) Copy   

•   Source: SciCrunch Registry

http://agbase.msstate.edu/cgi-bin/tools/goprofiler_select.pl

Service that provides a summary of GO annotations available for each species. The user provides a taxon id and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided.

Proper citation: GOProfiler (RRID:SCR_005683) Copy   

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http://www.pandora.cs.huji.ac.il/

With PANDORA, you can search for any non-uniform sets of proteins and detect subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA supports GO annotations as well as additional keywords (from UniProt Knowledgebase, InterPro, ENZYME, SCOP etc). It is also integrated into the ProtoNet system, thus allowing testing of thousands of automatically generated protein families. Note that PANDORA replaces the ProtoGO browser developed by the same group. Platform: Online tool

Proper citation: Pandora - Protein ANnotation Diagram ORiented Analysis (RRID:SCR_005686) Copy   

•   Source: SciCrunch Registry

http://mcbc.usm.edu/gofetcher/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 29, 2012. We developed a web application, GOfetcher, with a very comprehensive search facility for the GO project and a variety of output formats for the results. GOfetcher has three different levels for searching the GO: Quick Search, Advanced Search, and Upload Files for searching. The application includes a unique search option which generates gene information given a nucleotide or protein accession number which can then be used in generating gene ontology information. The output data in GOfetcher can be saved into several different formats; including spreadsheet, comma-separated values, and the Extensible Markup Language (XML) format. Platform: Online tool

Proper citation: GOfetcher (RRID:SCR_005681) Copy   

•   Source: SciCrunch Registry

http://llama.mshri.on.ca/gofish/GoFishWelcome.html

Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GoFish (RRID:SCR_005682) Copy   

•   Source: SciCrunch Registry

http://www.hcvdb.org/

The Hepatitis C Virus Database (HCVdb) is a cooperative project of several groups with the mission of providing to the scientific community studying the hepatitis C virus a comprehensive battery of informational and analytical tools. The Viral Bioinformatics Resource Center (VBRC), the Immune Epitope Database and Analysis Resource (IEDB), the Broad Institute Microbial Sequencing Center (MSC), and the Los Alamos HCV Sequence Database (HCV-LANL) are combining forces to acquire and annotate data on Hepatitis C virus, and to develop and utilize new tools to facilitate the study of this group of organisms.

Proper citation: Hepatitis C Virus Database (HCVdb) (RRID:SCR_005718) Copy   

•   Source: SciCrunch Registry

http://www.eie.gr/index-en.html

The National Hellenic Research Foundation (NHRF) is a multidisciplinary Research Centre established by Royal Decree on 9th October 1958. Its purpose is the organisation, finance and support of high-level research projects in the humanities and the natural sciences. The Humanities Institute cover a wide spectrum of study and research fields in Greek history and culture, contributing substantially and critically to the knowledge and promotion of Greek identity. The Natural Sciences Institutes perform basic and applied research in leading edge areas of science such as health, pharmaceuticals, environment, biotechnology and new materials. They develop innovative methods for solving complex problems facing Greek industry and they provide specialised services and know-how both to the public and private sector. The NHRF is governed by the Board of Directors and the Central Administration under the Director/Chairman of the Board.

Proper citation: National Hellenic Research Foundation (RRID:SCR_005719) Copy   

•   Source: SciCrunch Registry

http://www.utsouthwestern.edu/education/medical-school/departments/pathology/index.html

The Department of Pathology at UT Southwestern Medical Center is committed to its missions in diagnostics, research, teaching, and resident and fellowship training. Our facilities include approximately 54,000 square feet of lab and office space. Our Department comprises more than 100 of the most outstanding faculty in the country and more than 50 residents and fellows. We are home to more than a dozen graduate students at any given time. The Department of Pathology offers comprehensive, in-depth training in all of the various pathology disciplines, as well as a complete array of subspecialty fellowship programs. It is our view that a strong academic environment with access to state-of-the-art and newly emerging diagnostic technologies is essential to the preparation of any pathologist for professional life in the 21st century, regardless of the ultimate practice setting. Therefore, basic training in our program is enhanced by extensive exposure to modern molecular diagnostics, advanced flow cytometric analysis, and molecular cytogenetics. The Department provides diagnostic services in a variety of clinical settings that include a large county hospital (Parkland Memorial Hospital), two private University Hospitals (Zale-Lipshy and St. Paul), a tertiary care private pediatric hospital (Children''s Medical Center), a large university outpatient clinic (Aston Clinic), and the Dallas VA Medical Center, exposing our residents, fellows, and faculty to the full spectrum of human adult and pediatric disease.

Proper citation: UT Southwestern Medical Center Department of Pathology (RRID:SCR_005713) Copy   

•   Source: SciCrunch Registry

http://maq.sourceforge.net/maqview.shtml

A graphical read alignment viewer specifically designed for the Maq alignment file and allows you to see the mismatches, base qualities and mapping qualities. It is highly efficient in speed, memory and disk usage. Maqview is based on OpenGL and is known to work on both Mac OS X and Linux. Porting to Windows is in principle easy.

Proper citation: Maqview (RRID:SCR_005632) Copy   

•   Source: SciCrunch Registry

http://genome-www.stanford.edu/TMA/

Software Tools for High-Throughput Analysis and Archiving of Immunohistochemistry Staining Data Obtained with Tissue Microarrays.

Proper citation: Stanford TMA Software (RRID:SCR_005598) Copy   

•   Source: SciCrunch Registry

http://www.compbio.dundee.ac.uk/downloads/oxbench/

A suite of programs aimed at developers of alignment methods rather than end-users to assess the accuracy of multiple sequence alignment methods. It includes a reference database of protein multiple sequence alignments that were generated by consideration of protein three-dimensional structure.

Proper citation: OXBench (RRID:SCR_005591) Copy   

•   Source: SciCrunch Registry

http://www.solvetherapies.co.uk

Our hope and aims are to empower those affected by common life difficulties such as Anxiety, Depression, low Self-Esteem etc to overcome their obstacles and achieve their full and true potential. Our core approach is client-centred and we aim to convey to each client the ''core conditions'' of empathy, congruence and unconditional positive regard. Using Compassion focused Cognitive Behavioral Therapy (CBT), Acceptance and Commitment Therapy (ACT) among other approaches we gear all therapy treatments towards clients unique needs and goals. Passionate about research in all therapeutic and associated fields, we want to continue to keep our fingers on the pulse of developments in this area of work. We at Solve Therapies strive to empower all of our clients to choose helpful, rational thoughts and actions and to do so with less shame and self-criticism through the use of Cognitive Behavioural Therapy and Compassion-focused techniques. We offer a confidential, professional therapeutic service using Cognitive Behavioural Therapy and other forms of counseling/psychotherapy. All therapists are accredited and regulated by the British Association of Counselling & Psychotherapy (BACP) and/or British Association of Behavioural and Cognitive Psychotherapy (BABCP), the professional bodies who regulate, inform and ensure ethical practice. We also provide useful information on common difficulties and on how you can learn how to become your own therapist and manage your difficulties in the long term, with counselling venues throughout Northern Ireland including Belfast, Portrush, Antrim and Portglenone in order to provide flexibility for client appointments. ''''''S''''''olution-focused ''''''O''''''ptions ''''''L''''''ife-change ''''''V''''''alidation ''''''E''''''mpathy

Proper citation: Solve Therapies (RRID:SCR_005590) Copy   

•   Source: SciCrunch Registry

http://staden.sourceforge.net/

A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.

Proper citation: Staden Package (RRID:SCR_005629) Copy   

•   Source: SciCrunch Registry

http://www.esourceresearch.org/

Inside e-Source you will find 20 interactive chapters with authoritative answers to methodological questions on behavioral and social science research. With contributions from a team of international experts, this anthology provides the latest information on addressing emerging challenges in public health. Book contents include: Setting the Scene, Describing How, Explaining Why, What Works, Emerging Issues. Tables, Figures, Exercises and Examples are included. Login for enhanced functionality. Contents: * Appropriate Research Methods * ''Science'' in the Social Sciences * Design Decisions in Research * Theory Development * Social and Behavioral Theories * Sample Surveys * Social Survey Data Collection * Administrative Data Systems * Observational Studies * Qualitative Methods * Conversation Analysis * Software and Qualitative Analysis * Clinical Trials * Cluster Unit Randomized Trials * Ethical Challenges * Multilevel Modeling * Objective Measurement of Subjective Phenomena * Measuring Socioeconomic Status * Evaluating the Quality of Health Care * Patient-Reported Outcomes

Proper citation: e-Source: Behavioral and Social Sciences Research (RRID:SCR_005627) Copy   

•   Source: SciCrunch Registry

http://grants.nih.gov/podcasts/All_About_Grants/index.htm

The Office of Extramural Research (OER) presents conversations with NIH staff members. Designed for investigators, fellows, students, research administrators, and others, we provide insights on grant topics from those who live and breathe the information. In mp3 and updated monthly. Transcripts are also available. So You Wanna... Keep Up with What''''s Hot? Prepare a Successful Grant Application? Suggest a Topic? Understand How Your Grant is Reviewed? Be an NIH Investigator?

Proper citation: All About Grants Podcast (RRID:SCR_005621) Copy   

•   Source: SciCrunch Registry

http://www.hca-vision.com/product_spot.html

Software package for analysis of microarray images. Microarray spot detection and characterization software package which extracts numerical information from cDNA microarrays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPOT (RRID:SCR_005623) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/research-funding/training/index.shtml

A portal to the National Institute of Mental Health''s Research Training, Career Development, and Related Programs. Topics cover Resources for Applicants, Individual Fellowship Programs, Individual Career Development Programs, Institutional Training Programs, Additional Career Development/Training-Related Opportunities, and Training Programs to Increase Workforce Diversity.

Proper citation: NIMH Resources for Research Training and Career Development (RRID:SCR_005624) Copy   

•   Source: SciCrunch Registry

http://mesquiteproject.org/packages/chromaseq/

A software package in Mesquite that processes chromatograms, makes contigs, base calls, etc., using in part the programs Phred and Phrap.

Proper citation: Chromaseq (RRID:SCR_005587) Copy   

•   Source: SciCrunch Registry

https://github.com/phe-bioinformatics/snp-search/tree/master/test_data

A software tool that manages SNP data and outputs useful information which can be used to test important biological hypotheses.

Proper citation: snp-search (RRID:SCR_005618) Copy   

•   Source: SciCrunch Registry

http://slicer.org/

A free, open source software package for visualization and image analysis including registration, segmentation, and quantification of medical image data. Slicer provides a graphical user interface to a powerful set of tools so they can be used by end-user clinicians and researchers alike. 3D Slicer is natively designed to be available on multiple platforms, including Windows, Linux and Mac Os X. Slicer is based on VTK (http://public.kitware.com/vtk) and has a modular architecture for easy addition of new functionality. It uses an XML-based file format called MRML - Medical Reality Markup Language which can be used as an interchange format among medical imaging applications. Slicer is primarily written in C++ and Tcl.

Proper citation: 3D Slicer (RRID:SCR_005619) Copy   

•   Source: SciCrunch Registry