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http://www.scid4.org/

A diagnostic exam used to determine DSM-IV Axis I disorders (SCID-I) (major mental disorders) and Axis II disorders (SCID-II) (personality disorders). An Axis I SCID assessment with a psychiatric patient usually takes between 1 and 2 hours, depending on the complexity of the subject's psychiatric history and their ability to clearly describe episodes of current and past symptoms. A SCID with a non-psychiatric patient takes 1/2 hour to 1-1/2 hours. A SCID-II personality assessment takes about 1/2 to 1 hour. The instrument was designed to be administered by a clinician or trained mental health professional. (Adapter from Wikipedia)

Proper citation: Structured Clinical Interview for DSM-IV (RRID:SCR_003682) Copy   

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http://www.dementiatoday.com/wp-content/uploads/2012/06/MiniMentalStateExamination.pdf

A 30 question assessment test to screen patients for cognitive impairment that is commonly used in medicine to screen for dementia. It is also used to estimate the severity of cognitive impairment and to follow the course of cognitive changes in an individual over time, thus making it an effective way to document an individual's response to treatment. It takes about 10 minutes and examines functions including arithmetic, memory and orientation.

Proper citation: Mini-Mental State Examination (RRID:SCR_003681) Copy   

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http://psychology-tools.com/major-depression-inventory/

A 12 item self-report mood assessment developed by the World Health Organisation that is able to generate an ICD-10 or DSM-IV diagnosis of clinical depression in addition to an estimate of symptom severity. Scoring: * Mild depression: A score of 4 or 5 in two of the first three items. Plus a score of at least 3 on two or three of the last seven items. * Moderate depression: A score of 4 or 5 in two or three of the first three items. Plus a score of at least 3 on four of the last seven items. * Severe depression: A score of 4 or 5 in all of the first three items. Plus a score of at least 3 on five or more of the last seven items. * Major depression: The number of items is reduced to nine, as Item 4 is part of Item 5. Include whichever of the two items has the highest score (item 4 or 5). A score on at least five items is required, to be scored as follows: the score on the first three items must be at least 4, and on the other items at least 3. Either Item 1 or 2 must have a score of 4 or 5.

Proper citation: Major Depression Inventory (RRID:SCR_003688) Copy   

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http://www.teenmentalhealth.org/images/resources/CAPN_11Item_KADS.pdf

A psychological self-rating scale developed by Dalhousie University professor of psychiatry Stan Kutcher, to assess the level of depression in adolescents. While there are some variations, the 11-item version of the KADS is the most commonly used and most thoroughly verified for efficacy in monitoring outcomes in adolescents who are receiving treatment for major depressive disorder. Its items are worded using standard and colloquial terminology, and responses are scored on a simple 4 choice scale. There are ten questions about depression symptom frequency that the patient rates on a straight 4 point scale according to the following choices: hardly ever, much of the time, most of the time, all the time, and one question relating to the severity of suicidal ideation. Scores on the test range from 0 to 33. Unlike some rating scales, there is no threshold for sub-clinical presentation, or ranges for mild, moderate, and severe symptoms. Higher scores simply indicate more severe current depression symptoms. (Adapted from Wikipedia)

Proper citation: Kutcher Adolescent Depression Scale (RRID:SCR_003687) Copy   

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http://www.ebi.ac.uk/Tools/

The European Bioinformatics Institute (EBI) toolbox area provides a comprehensive range of tools for the field of bioinformatics. These are subdivided into categories in the left menu for convenience. EBI has developed a large number of very useful bioinformatics tools. A few examples include: - Similarity & Homology - the BLAST or FASTA programs can be used to look for sequence similarity and infer homology. - Protein Functional Analysis - InterProScan can be used to search for motifs in your protein sequence. - Proteomic Services NEW - UniProt DAS server allows researchers to show their research results in the context of UniProtKB/Swiss-Prot annotation. - Sequence Analysis - ClustalW2 a sequence alignment tool. - Structural Analysis - MSDfold can be used to query your protein structure and compare it to those in the Protein Data Bank (PDB). - Web Services - provide programmatic access to the various databases and retrieval/analysis services EBI provides. - Tools Miscellaneous - Expression Profiler a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Sponsors: This resource is sponsored by EBI.

Proper citation: Toolbox at the European Bioinformatics Institute (RRID:SCR_002872) Copy   

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http://psychology-tools.com/cast/

Assessment test developed by the Autism Research Centre at the University of Cambridge, for assessing the severity of autism spectrum symptoms in children. This assessment is usually used with children aged from 4-11 years of age.

Proper citation: Childhood Autism Spectrum Test (RRID:SCR_003322) Copy   

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http://www.fresno.ucsf.edu/pediatrics/downloads/edinburghscale.pdf

A 10 item assessment scale developed to identify women who have postpartum depression (PPD). Items of the scale correspond to various clinical depression symptoms, such as guilt feeling, sleep disturbance, low energy, anhedonia, and suicidal ideation. Overall assessment is done by total score, which is determined by adding together the scores for each of the 10 items. Higher scores indicate more depressive symptoms. The EPDS may be used within 8 weeks postpartum and it also can be applied for depression screening during pregnancy. (Adapted from Wikipedia) Scoring: * 0-9 Not Likely to Have Depression * 10-30 Likely to Have Depression

Proper citation: Edinburgh Postnatal Depression Scale (RRID:SCR_003685) Copy   

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http://www.biostat.wustl.edu/~adrc/cdrpgm/

A numeric scale used to quantify the severity of symptoms of dementia (i.e. its stage). Using a structured-interview protocol, a qualified health professional assesses a patient's cognitive and functional performance in six areas: memory, orientation, judgment and problem solving, community affairs, home and hobbies, and personal care. Scores in each of these are combined to obtain a composite score ranging from 0 through 3. (Adapted from Wikipedia)

Proper citation: Clinical Dementia Rating (RRID:SCR_003678) Copy   

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http://www.brain-connectivity-toolbox.net

A large selection of complex network measures in Matlab that are increasingly used to characterize structural and functional brain connectivity datasets. Several people have contributed to the toolbox, and if you wish to contribute with a new function or set of functions, please contact Olaf Sporns. All efforts have been made to avoid errors, but users are strongly urged to independently verify the accuracy and suitability of toolbox functions for the chosen application. Please report bugs or substantial improvements.

Proper citation: Brain Connectivity Toolbox (RRID:SCR_004841) Copy   

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http://www.mindupload.org/index.php?tab=2&sub=0

A database-based neuron simulation tool. An innovative approach to large-scale, biologically plausible, neural-network simulation library. Based on data structures and methods directly coded into database, information flow implying separation of data representing neurons, conceived to share load on multiple machines and calibrating operational load on each machine.

Proper citation: splitneuron (RRID:SCR_005001) Copy   

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http://disco.neuinfo.org

DISCO is an information integration approach designed to facilitate interoperation among Internet resources. It consists of a set of tools and services that allows resource providers who maintain information to share it with automated systems such as NIF. NIF is then able to harvest the information and keep those sets of information up-to-date. How is this accomplished? By using a series of files and/or scripts which are then placed in the root directory of the resource developer''s resource. (NIF can also host the files on its servers and crawl for changes there.) Once the files of the resource providers are in place, and DISCO is notified, the DISCO server can then recognize and consume the information shared, providing machine understandable information to NIF Integrator Servers (also known as Aggregators) about your resource. What can DISCO do for my resource? * Inform search engines about your resource and keep your NIF Registry resource description up-to-date. * Expose your data (semi-structured datasets or fields within your structured database) through NIF''s Data Federation you choose what data will be shared. * Create links from an NCBI database (e.g., PubMed, Protein, Nucleotide, etc.) to your data records in NIF using Entrez LinkOut. * Advertise your terminology or ontological information. * Share your resource''s news with the NIF community., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DISCO (RRID:SCR_004586) Copy   

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http://www.yandell-lab.org/software/maker.html

Software genome annotation pipeline. Portable and easily configurable genome annotation pipeline. Used to allow smaller eukaryotic and prokaryotic genomeprojects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence based quality values.

Proper citation: MAKER (RRID:SCR_005309) Copy   

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http://www.sanger.ac.uk/resources/software/alien_hunter/

Alien_hunter is an application for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. An IVOM approach exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared to fixed-order methods. Optionally the predictions can be parsed into a 2-state 2nd order Hidden Markov Model (HMM), in a change-point detection framework, to optimize the localization of the boundaries of the predicted regions. The predictions (embl format) can be automatically loaded into the freely available Artemis genome viewer.

Proper citation: Alien hunter (RRID:SCR_004575) Copy   

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http://www.uni-bonn.de/~umt70e/soft.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that calculates the sample size required for obtaining a prescribed power against a specified alternative for TDT. (entry from Genetic Analysis Software)

Proper citation: TDTPOWER (RRID:SCR_005021) Copy   

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http://www.gotaxexplorer.de/

The Functional Similarity Search Tool (FSST) has been implemented for comparing user defined sets of annotated entities. FSST supports the computation of functional similarity scores based on an individual ontology and of combined scores. Its multi-threaded Java implementation takes advantage of symmetric multi-processing computers, decreasing runtime considerably. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: FSST - Functional Similarity Search Tool (RRID:SCR_005819) Copy   

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https://reich.hms.harvard.edu/software

EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker''s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. Source code, documentation and executables for using EIGENSOFT 3.0 on a Linux platform can be downloaded. New features of EIGENSOFT 3.0 include supporting either 32-bit or 64-bit Linux machines, a utility to merge different data sets, a utility to identify related samples (accounting for population structure), and supporting multiple file formats for EIGENSTRAT stratification correction.

Proper citation: Eigensoft (RRID:SCR_004965) Copy   

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http://ugene.unipro.ru/

A multiplatform open-source software to assist molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality.

Proper citation: Unipro UGENE (RRID:SCR_005579) Copy   

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http://www.biological-networks.org/p/outliers/

Software that performs a morphology-based approach for the automatic identification of outlier neurons based on neuronal tree structures. This tool was used by Zawadzki et al. (2012), who reported on and its application to the NeuroMorpho database. For the analysis, each neuron is represented by a feature vector composed of 20 measurements, which are projected into lower dimensional space with PCA. Bivariate kernel density estimation is then used to obtain a probability distribution for cells. Cells with high probabilities are understood as archetypes, while those with the small probabilities are classified as outliers. Further details about the method and its application in other domains can be found in Costa et al. (2009) and Echtermeyer et al. (2011). This version requires Matlab (Mathworks Inc, Natick, USA) and allows the user to apply the workflow using a graphical user interface.

Proper citation: DONE: Detection of Outlier NEurons (RRID:SCR_005299) Copy   

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http://www.kickstarter.com/

Kickstarter is the world''s largest funding platform for creative projects. Every week, tens of thousands of amazing people pledge millions of dollars to projects from the worlds of music, film, art, technology, design, food, publishing and other creative fields. A new form of commerce and patronage. This is not about investment or lending. Project creators keep 100% ownership and control over their work. Instead, they offer products and experiences that are unique to each project. All or nothing funding. On Kickstarter, a project must reach its funding goal before time runs out or no money changes hands. Why? It protects everyone involved. Creators aren''t expected to develop their project without necessary funds, and it allows anyone to test concepts without risk. Each and every project is the independent creation of someone like you. Projects are big and small, serious and whimsical, traditional and experimental. They''re inspiring, entertaining and unbelievably diverse. We hope you agree... Welcome to Kickstarter!

Proper citation: Kickstarter (RRID:SCR_004246) Copy   

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http://genetics.agrsci.dk/~bg/popgen/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that calculates a number of different genetic identities, phylogeny reconstructing measures, and distance reconstructing measures (entry from Genetic Analysis Software)

Proper citation: POPDIST (RRID:SCR_004904) Copy   

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