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http://www.utsa.edu/claibornelab/

The long-term goals of my research are to understand the relationship between neuronal structure and function, and to elucidate the factors that affect neuronal morphology and function over the lifespan of the mammal. Currently we are examining 1) the effects of synaptic activity on neuronal development; 2) the effects of estrogen on neuronal morphology and on learning and memory; and, 3) the effects of aging on neuronal structure and function. We have focused our efforts on single neurons in the hippocampal formation, a region that is critical for certain forms of learning and memory in rodents and humans. From the portal, you may click on a cell in your region of interest to see the complete database of cells from that region. You may also explore the Neuron Database: * Comparative Electrotonic Analysis of Three Classes of Rat Hippocampal Neurons. (Raw data available) * Quantitative, three-dimensional analysis of granule cell dendrites in the rat dentate gyrus. * Dendritic Growth and Regression in Rat Dentate Granule Cells During Late Postnatal Development.(Raw data available) * A light and electron microscopic analysis of the mossy fibers of the rat dentate gyrus.

Proper citation: University of Texas at San Antonio Laboratory of Professor Brenda Claiborne (RRID:SCR_008064) Copy   

•   Source: SciCrunch Registry

http://www.cambridgesoft.com/databases/login/?serviceid=128

THIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. ChemBioFinder.com is an online chemistry and biology reference database. With more than 500,000 compounds indexed and linked to other web sites, it provides a wealth of chemical information for professional chemists and students alike. ChemBioFinder.com is the gateway to all databases available from CambridgeSoft.
At ChemBioFinder.com, a subscriber can search for compounds by name, CAS Registry Number, molecular formula or weight, or by structure (exact and substructure). Successful searches return a basic profile of molecules indexed by this site. The profile contains the name, molecular formula and weight, CAS Registry Number, SMILES and InChI strings for each located compound, and lists the databases which contain entries for the located compound(s). Free trials to any of these databases are available, as are annual subscriptions for continuous use of the contents.
Users of ChemBioFinder.com are allowed 5 free searches before we request them to register with us as a cambridgesoft.com website user. The CambridgeSoft user account is free and will give you access to a growing list of products and services which includes, our quarterly print publication Chem & Bio News, frequent webinars, white papers and articles on all our offerings. Set up is fast & easy.
For ChemFinder.com users:
ChemFinder.Com has become ChemBioFinder.Com and has a whole new look and layout. This is part of a gradual redesign of the entire CambridgeSoft website. Here are some of the changes that were made to improve the vital information presented here to the scientific community:
1. Search results show the ChemBioFinder databases which have entries for the compound(s), and indicate the databases to which the logged in user has active subscriptions.
2. There are hyperlinks to the detailed records in the databases with active subscriptions.
3. Search results provide the name, molecular formula and weight, CAS Registry Number, SMILES and InChI strings for the compound.
4. Physical properties are no longer provided unless the user has a subscription to ChemIndex or other CambridgeSoft online databases that provide this information. Many of our products come with one year subscriptions to ChemIndex as part of the package. So you may actually be entitled to a subscription and dont realize it.

Proper citation: ChemBioFinder (RRID:SCR_008180) Copy   

•   Source: SciCrunch Registry

http://www.snl.salk.edu/~jude/neuron_exchange/

This resource contains to MATLAB code to make and show videos that can be acquired for free. Data for the movies came from a Macaque attention task. Data on this page came from the multiple-object tracking attention task in a Macaque: The monkeys fixated the white dot at the center of the computer monitor, and four striped stimuli appeared. Their eye position was monitored using an IR camera. The red cross shows where the eyes were pointing throughout each trial. The circle shows the location of the receptive field of the neuron under study during the recording. At the beginning of each trial, either one or two of the stimuli were highlighted, indicating to the monkey that they were the targets of attention. The stimuli then moved to new locations and paused, with one stimulus in the receptive field. After a brief pause, they moved to new locations and the fixation point disappeared. The monkey was rewarded with juice if it then looked at the cued targets. Attention Dask Demo (Avi File) contains Matlab code to make and show movies. Publication from this Dataset: * Differential attention-dependent response modulation across cell classes in macaque visual area V4. JF Mitchell, KA Sundberg, JH Reynolds. Neuron, 2007, 55. 131-141. * Supplemental Material, Neuron, 2007, 55. 131-141. :A Subset of data can be downloaded with analysis routines (easiest to download whole set with full subdirectory structure). Additionally, neuron data files can also be downloaded. :* Routines for Fano Factor, Autocorrelation, and Power Spectra (poster above): :o Plots Spike Waveform and Tests if Significant Visual Response: basic_info.m :o Firing Rate and Fano Factor Analysis (Mitchell et. al, 2007): rate_fano_psth.m :* Routines for Spike-LFP Coherence: :o Spike-LFP Coherence with Rate Normalization (attempting Womelsdorf & Fries, Cosyne, 2008): rate_normalized_coherence.m Sponsors: This work was supported by a grant from the National Eye Institute (EY016161, J.F.M. and J.H.R.), a National Institutes of Health Training Fellowship (J.F.M.), and a National Science Foundation Graduate Research Fellowship (K.A.S.).

Proper citation: Salk Institute for Biological Studies: Jude Mitchells Neuron Exchange and Matlab Analysis (RRID:SCR_008055) Copy   

•   Source: SciCrunch Registry

http://www.nimh.nih.gov/funding/clinical-trials-for-researchers/practical/stard/index.shtml

A nationwide public health clinical trial conducted to determine the effectiveness of different treatments for people with major depression, in both primary and specialty care settings, who have not responded to initial treatment with an antidepressant. This is the largest and longest study ever done to evaluate depression treatment. The study is completed and no longer recruiting participants. Each of the four levels of the study tested a different medication or medication combination. The primary goal of each level was to determine if the treatment used during that level could adequately treat participants����?? major depressive disorder (MDD). Those who did not become symptom-free could proceed to the next level of treatment. The design of the STAR*D study reflects what is done in clinical practice because it allowed study participants to choose certain treatment strategies most acceptable to them and limited the randomization of each participant only to his/her range of acceptable treatment strategies. No prior studies have evaluated the different treatment strategies in broadly defined participant groups treated in diverse care settings. Over a seven-year period, the study enrolled 4,041 outpatients, ages 18-75 years, from 41 clinical sites around the country, which included both specialty care settings and primary medical care settings. Participants represented a broad range of ethnic and socioeconomic groups. All participants were diagnosed with MDD, were already seeking care at one of these sites, and were referred to the trial by their doctors. * STAR*D Study Medications: Citalopram (Celexa), Sertraline (Zoloft), Bupropion SR (Wellbutrin SR), Venlafaxine XR (Effexor XR), Buspirone (BuSpar), Mirtazapine (Remeron), Triiodothyronine (T3) (Cytomel), Nortriptyline (Pamelor, Aventyl), Tranylcypromine (Parnate), Lithium (Eskalith, Lithobid) *STAR*D Talk Therapy:Cognitive Therapy

Proper citation: Sequenced Treatment Alternatives to Relieve Depression Study (RRID:SCR_008051) Copy   

•   Source: SciCrunch Registry

http://openwetware.org/wiki/Main_Page

OpenWetWare is an effort to promote the sharing of information, know-how, and wisdom among researchers and groups who are working in biology & biological engineering. OWW provides a place for labs, individuals, and groups to organize their own information and collaborate with others easily and efficiently. In the process, the hope is that OWW will not only lead to greater collaboration between member groups, but also provide a useful information portal to our colleagues, and ultimately the rest of the world. OWW''s approaches to achieve their goals: # Lower the technical barriers to sharing and dissemination of knowledge in biological research # Build a community of researchers in biology and biological engineering that values, practices, and innovates the open sharing of information # Integrate OpenWetWare into existing and future reward structures in research

Proper citation: OpenWetWare (RRID:SCR_008053) 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://qiime.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2023.Software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data, but also supporting analysis of other types of data. QIMME analyzes and transforms raw sequencing data generated on Illumina or other platforms to publication quality graphics and statistics.

Proper citation: QIIME (RRID:SCR_008249) Copy   

•   Source: SciCrunch Registry

http://www.jax.org/imr/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 08, 2012. The function of the IMR is to select, import, cryopreserve, maintain, and distribute these important strains of mice to the research community. To improve their value for research, the IMR also undertakes genetic development of stocks, such as transferring mutant genes or transgenes to defined genetic backgrounds and combining transgenes and/or targeted mutations to create new mouse models for research. The function of the IMR is to: * select biomedically important stocks of transgenic, chemically induced, and targeted mutant mice * import these stocks into the Jackson Laboratory by rederivation procedures that rid them of any pathogens they might carry * cryopreserve embryos from these stocks to protect them against accidental loss and genetic contamination * backcross the mutation onto an inbred strain, if necessary * distribute them to the scientific community More than 1000 mutant stocks have been accepted by the IMR from 1992 through December 2006. Current holdings include models for research on cancer; breast cancer; immunological and inflammatory diseases; neurological diseases; behavioral, cardiovascular and heart diseases; developmental, metabolic and other diseases; reporter (e.g., GFP) and recombinase (e.g., cre/loxP) strains. About eight strains a month are being added to the IMR holdings. Research is being conducted on improved methods for assisted reproduction and speed congenic production. Most of the targeted mutants arrive on a mixed 129xC57BL/6 genetic background, and as many of these as possible are backcrossed onto an inbred strain (usually C57BL/6J). In addition, new mouse models are being created by intercrossing carriers of specific transgenes and/or targeted mutations. Simple sequence length polymorphism DNA markers are being used to characterize and evaluate differences between inbred strains, substrains, and embryonic stem cell lines.

Proper citation: Induced Mutant Resource (RRID:SCR_008366) Copy   

•   Source: SciCrunch Registry

http://www.osc.riken.jp/english/

Omics Science Center is aiming to develop a comprehensive system called Life Science Accelerator(LSA) for the advancement of omics research. The LSA is a comprehensive system consists of biological resources, human resources, technologies, know-how, and essential administrative ability. Ultimate goal of LSA is to support and accelerate the advancement in life science research. Omics is the comprehensive study of molecules in living organisms. The complete sequencing of genomes (the complete set of genes in an organism) has enabled rapid developments in the collection and analysis of various types of comprehensive molecular data such as transcriptomes (the complete set of gene expression data) and proteomes (the complete set of intracellular proteins). Fundamental omics research aims to link these omics data to molecular networks and pathways in order to advance the understanding of biological phenomena as systems at the molecular level.

Proper citation: RIKEN Omics Science Center (RRID:SCR_008241) Copy   

•   Source: SciCrunch Registry

http://www.repairgenes.org/index.shtml

The aim of the repairGenes site is to be a source of information about DNA repair genes and a useful resource for research on DNA repair. At the moment, the site contains information about a number of DNA repair genes from a set of selected species. The information is organized by organism and by biological process term as defined by the Gene Ontology (GO) project. The coverage of DNA repair genes is not complete, but hopefully it satisfies to demonstrate the concept and generate ideas for future versions of the system. At present, the raw data about DNA repair genes is extracted from the SWISS-PROT database, and categorized using the GO system. SWISS-PROT entries are being annotated by the Gene Ontology Annotation project at EBI. GOA is an ongoing project which will become more complete with time. As more data is released, this will be fed into repairGenes to keep it up-to-date. In future versions, the user will be able to search freely among organisms and categories of repair genes, enabling easy comparisons between species. For a taste of this, please have a look at the overview of repair genes from five major organisms. The amount of information in the system will be increased and the quality will be improved in the future. So will the features of the system.

Proper citation: repairGenes (RRID:SCR_008240) 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.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://www.liden.cc/Visionary/

It is a dictionary for terminology used in the study of human and animal vision. It includes terms from the areas of biological and machine vision, visual psychophysics, visual neuroscience and other related fields. Sponsors: Visionary is sponsored by Educational Software for Autism.

Proper citation: Visionary: A Dictionary for the Study of Vision (RRID:SCR_008307) 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

http://biq-analyzer.bioinf.mpi-sb.mpg.de

BiQ Analyzer is a software tool for easy visualization and quality control of DNA methylation data from bisulfite sequencing. Highlights: - End-to-end support of the analysis process: from raw sequence files to a comprehensive documentation and visualization. - Automatically generate publication-quality lollipop diagrams (show example.) - Integrated 1-click multiple sequence alignment. - Automated CpG highlighting- never spend your time highlighting CpGs by hand anymore. - Open electropherogram files to check for sequencing problems (requires an electropherogram viewer such as Chromas LITE.) - Generate MethDB-compatible DNA methylation files for database submission. - Factor 5 speedup of sequence analysis while at the same time achieving better data quality. Intended users: - Anyone who works with DNA methylation data from bisulfite sequencing. - Occasional users as well as experts (the former will benefit from the help that the program gives in order to achieve a good quality management whereas the latter will save hours and days of tedious work.) Sponsors: This resource is supported by the Max Planck Institute. Keywords: Software, Visualization, DNA, Methylation, Data, Bisulfite, Sequencing, Electropherogram, Analysis,

Proper citation: BiQ Analyzer: A Software Tool for DNA Methylation Analysis (RRID:SCR_008423) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/PostGenomics/S_pombe/

The laboratory studies global gene expression programs in fission yeast (S. pombe). They apply a wide range of integrated approaches to analyse regulatory networks during cell proliferation, differentiation and quiescence including genetic and environmental perturbations. They are also interested in genetic diversity, genome evolution, and the complex interactions between genotypes, phenotypes, and the environment. The relative simplicity of the yeast cell promises a deeply satisfying, systems-level understanding of its inner workings within our life time Sponsors: This research is mainly funded by Cancer Research UK and the EC FP7 PhenOxiGEn project. Keywords: Gene, Expression, S.pombe, Yeast, Cell, Proliferation, Differentiation, Environmental, Genetic, Diversity, Genome, Evolution, Genotype, Phenotype, Environment,

Proper citation: Bahler Laboratory: Genome Regulation (RRID:SCR_008422) Copy   

•   Source: SciCrunch Registry

http://www.cabiatl.com/mricro/

MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyze MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms. Some features of MRIcro are: - Converts medical images to SPM friendly Analyze format. - View Analyze format images (big or little endian). - Create Analyze format headers (big or little endian). - Create 3D regions of interest (with computed volume & intensity). - Overlap multiple regions of interest. - Rotate images to match SPM template images. - Export images to BMP, JPEG, PNG or TIF format. - Yoked images: linked viewing of multiple images (e.g. view same coordinates of PET and MRI scans). Users familiar with other Windows programs will find that this software is fairly straightforward to use. Resting the mouse cursor over a button will cause a text hint to appear over the button. However, a tutorial with a step by step guide of how to use MRIcro with SPM is available.

Proper citation: MRIcro Software (RRID:SCR_008264) Copy   

•   Source: SciCrunch Registry

http://www.amber.org.au/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 6, 2016. AMBeR's aim is to bring together Australia's unique resources for genetic epidemiology and genomics with high level expertise in bioinformatics and statistical science, conduct advanced methodological research, develop new research capacity and competitiveness in cutting-edge techniques, bring them to bear on important medical research problems, train young Australians in bioinformatics and advanced biostatistics, and transfer this expertise to the medical research community.

Proper citation: Australian Medical Bioinformatics Resource (RRID:SCR_008385) Copy   

•   Source: SciCrunch Registry

http://www.nia.nih.gov/research/dab/interventions-testing-program-itp

NIA''s ITP is a multi-institutional study investigating treatments with the potential to exte nd lifespan and delay disease and dysfunction in mice. Priority consideration will be given to the treatments that are easily obtainable, reasonably priced, and can be delivered in the diet (preferred) or water. Interventions that require labor intensive forms of administration, such as daily injections or gavage, are not feasible within the design of the ITP. Treatments currently under study include: - Pharmaceuticals - Nutraceuticals - Foods - Diets - Dietary supplements - Plant extracts - Hormones - Peptides - Amino acids - Chelators - Redox agents - Other agents or mixtures of agents Although the mice involved in this study will be housed at the University of Michigan, the Jackson Laboratories, and the University of Texas Health Sciences Center at San Antonio, the project is designed to involve collaborations with investigators at any university, institute, or other organization that has ideas about pharmacological interventions that might decelerate aging and wishes to test these in a lifespan study of mice. Sponsors: This program is supported by the National Institute of Aging.

Proper citation: Interventions Testing Program (RRID:SCR_008266) Copy   

•   Source: SciCrunch Registry

http://www.cdc.gov/nccdphp/ace/

A clinical study linking childhood maltreatment and later-life health and well-being. As a collaboration between the Centers for Disease Control and Prevention and Kaiser Permanente''s Health Appraisal Clinic in San Diego, Health Maintenance Organization (HMO) members undergoing a comprehensive physical examination provided detailed information about their childhood experience of abuse, neglect, and family dysfunction. Over 17,000 members chose to participate. To date, over 50 scientific articles have been published and over 100 conference and workshop presentations have been made. Future Directions: The ACE study is now in its 10th year and the prospective phase is currently underway. In this ongoing stage of the study, data are being gathered from various sources including outpatient medical records, pharmacy utilization records, and hospital discharge records to track the subsequent health outcomes and health care use of ACE Study participants. In addition, an examination of National Death Index records will be conducted to establish the relationship between ACE and mortality among the ACE Study population. The ACE Study findings suggest that these experiences are major risk factors for the leading causes of illness and death as well as poor quality of life in the United States. Progress in preventing and recovering from the nation''s worst health and social problems is likely to benefit from the understanding that many of these problems arise as a consequence of adverse childhood experiences. :Sponsors: This resource is supported by the Centers for Disease Control and Prevention and the Kaiser Permanente''s Health Appraisal Clinic in San Diego.

Proper citation: Adverse Childhood Experiences Study (RRID:SCR_008382) Copy   

•   Source: SciCrunch Registry