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http://cbi.labri.fr/Genolevures

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. It provides annotated sequence data and classifications for the genomes of eighteen species of hemiascomycete yeasts, including nine complete genomes. The Gnolevures web resources provides genetic element pages, orthologs defined by syntenic homology, protein families, a genome browser for interspecies comparison, and data sets for downloading. An advanced search facility permits a number of criterion-based and full text queries. Classification data, including protein families and orthologs, and the most up-to-date genome annotations, are for the most part not available in general-purpose sequence data bases such as EMBL/GenBank/DDBJ.

Proper citation: Genolevures (RRID:SCR_013173) Copy   

•   Source: SciCrunch Registry

https://itunes.apple.com/be/app/3d-brain/id331399332?mt=8

iPhone and iPad app that provides a good overview of the brain and its structures allowing you to rotate and zoom around 29 interactive structures with your touch screen. Discover how each brain region functions, what happens when it is injured, and how it is involved in mental illness. Each detailed structure comes with information on functions, disorders, brain damage, case studies, and links to modern research. Compatible with iPhone, iPod touch and iPad. Requires iOS 3.0 or later.

Proper citation: 3D Brain (RRID:SCR_013138) Copy   

•   Source: SciCrunch Registry

http://www.gene.affrc.go.jp/index_en.php

Research Center of Genetic Resources is central coordinating institute in Japan for conservation of plants, microorganisms, and animals related to agriculture. NARO Genebank coordinates this activity in collaboration with network of institutes throughout Japan. Conducts exploration, collection, characterization, preservation, and distribution service of microorganism genetic resources, animal genetic resources raised in Japan, and plant genetic resources.

Proper citation: Japanese Research Center of Genetic Resources NARO Genebank project (RRID:SCR_013259) Copy   

•   Source: SciCrunch Registry

http://nipy.org

Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration.

Proper citation: Neuroimaging in Python (RRID:SCR_013141) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pia2/

A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome.

Proper citation: PIA (RRID:SCR_013267) Copy   

•   Source: SciCrunch Registry

http://www.grc.nia.nih.gov/branches/blsa/blsanew.htm

America''s longest-running scientific study of human aging, begun in 1958. BLSA scientists are learning what happens as people age and how to sort out changes due to aging from those due to disease or other causes. More than 1,400 men and women are study volunteers. They range in age from their 20s to their 90s. This study is currently recruiting healthy seniors over 70.

Proper citation: Baltimore Longitudinal Study of Aging (BLSA) (RRID:SCR_013148) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/wgsim

A small tool for simulating sequence reads from a reference genome.

Proper citation: Wgsim (RRID:SCR_013269) Copy   

•   Source: SciCrunch Registry

http://tripod.nih.gov/

Tripod is a user-friendly chemical genomics browser that is currently being developed by the informatics group at the NIH Chemical Genomics Center. The main goal of Tripod is to facilitate easy access to chemical and biological data in an intuitive, user-friendly tool. To this end, the development of Tripod is inspired by the ubiquitous iTunes software, whereby browsing and managing of media contents are being adapted to chemical and biological data.

Proper citation: Tripod (RRID:SCR_013147) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/SOAPdenovo-Trans.html

A de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAPdenovo-Trans (RRID:SCR_013268) Copy   

•   Source: SciCrunch Registry

http://www.kennedykrieger.org/kki_2nd_inside.jsp?pid=3

Kennedy Krieger Institute is an institution dedicated to improving the lives of children and adolescents with pediatric developmental disabilities through patient care, special education, research, and professional training. Kennedy Kriegers clinical programs offer an interdisciplinary approach in treatment tailored to the individual needs of each child. Services include over 40 outpatient clinics; neurobehavioral, rehabilitation, and pediatric feeding disorders inpatient units; plus several home and community programs providing services to assist families. At Kennedy Krieger, there is no shortage of clinical programs to meet the specialized needs of children and adolescents with developmental disabilities. More than 35 different outpatient clinics, three inpatient units, several home and community programs and clinical laboratories all address the specific conditions of children with a wide range of disorders. Kennedy Krieger is recognized for its range of services in areas including autism, cerebral palsy, spina bifida, neurorehabilitation and feeding disorders. Kennedy Krieger school, is a nationally recognized Blue Ribbon School of Excellence, and is a leader in providing model programs of innovative education for children, adolescents and young adults with a wide range of learning, emotional, physical, neurological, and developmental disabilities. Faculty at Kennedy Krieger are among some of the worlds leading experts in this field and are attuned to the special needs of this population. These faculty have made crucial medical discoveries leading to innovative treatments and have improved the lives of individuals with disabilities. In addition to providing evaluation, rehabilitation, educational services and cutting edge research on behalf of children with brain related disabilities, Kennedy Krieger also provides professional training by renowned experts dedicated to increasing the number of qualified specialists in the United States and abroad. Children treated at Kennedy Krieger are seen by a variety of health care professionals working together in one or more of the Institutes clinical disciplines or departments. These highly trained professionals work directly with the Institutes medical staff to provide coordinated, interdisciplinary care tailored to the special needs of each child. This interdisciplinary approach puts Kennedy Krieger at the forefront in providing patient care for individuals with multiple developmental disabilities. Additionally, Kennedy Krieger Institutes Department of Special Education includes a number of programs that offer service to children with disabilities in a variety of settings. Kennedy Krieger School programs offer special education and related services to students aged 3-21 in three day-school settings and in partnership settings within public schools. For your convenience, a list of diagnoses/disorders treated at Kennedy Krieger Institute has been compiled to provide helpful related information for each diagnosis/disorder and include definitions, symptoms, treatment programs available at Kennedy Krieger, research being conducted at Kennedy Krieger, press releases, Potential articles and links to other helpful additional resources and websites outside the Institute.

Proper citation: Kennedy Krieger Institute: Diagnoses/Disorders (RRID:SCR_013260) Copy   

•   Source: SciCrunch Registry

http://www.ucdenver.edu/academics/colleges/medicalschool/centers/tastesmell/Pages/software.aspx

:GLOM MAP was written for MATLAB, it works equally as well on the PC as on the MAC. GLOM MAP consists of two components: 1. OBS can be used to map the location of glomeruli in transverse sections of the olfactory bulb. 2. GDB can be used to transform the OBS data and to analyze the collected glomerular activity data. This data can be scored and mapped in the radial and anterio-posterior dimensions as discussed in Salcedo et al, 2005. :

Proper citation: GLOM MAP is a toolbox written for the MATLAB development enviroment (RRID:SCR_013274) Copy   

•   Source: SciCrunch Registry

http://www.genesigdb.org

Database of traceable, standardized, annotated gene signatures which have been manually curated from publications that are indexed in PubMed. The Advanced Gene Search will perform a One-tailed Fisher Exact Test (which is equivalent to Hypergeometric Distribution) to test if your gene list is over-represented in any gene signature in GeneSigDB. Gene expression studies typically result in a list of genes (gene signature) which reflect the many biological pathways that are concurrently active. We have created a Gene Signature Data Base (GeneSigDB) of published gene expression signatures or gene sets which we have manually extracted from published literature. GeneSigDB was creating following a thorough search of PubMed using defined set of cancer gene signature search terms. We would be delighted to accept or update your gene signature. Please fill out the form as best you can. We will contact you when we get it and will be happy to work with you to ensure we accurately report your signature. GeneSigDB is capable of providing its functionality through a Java RESTful web service.

Proper citation: GeneSigDB (RRID:SCR_013275) Copy   

•   Source: SciCrunch Registry

http://bis.zju.edu.cn/pnatdb/

Natural Antisense Transcripts (NATs), a kind of regulatory RNAs, occur prevalently in plant genomes and play significant roles in physiological and/or pathological processes. PlantNATsDB (Plant Natural Antisense Transcripts DataBase) is a platform for annotating and discovering NATs by integrating various data sources involving approximately 2 million NAT pairs in 69 plant species. PlantNATsDB also provides an integrative, interactive and information-rich web graphical interface to display multidimensional data, and facilitate plant research community and the discovery of functional NATs. GO annotation and high-throughput small RNA sequencing data currently available were integrated to investigate the biological function of NATs. A ''''Gene Set Analysis'''' module based on GO annotation was designed to dig out the statistical significantly overrepresented GO categories from the specific NAT network. PlantNATsDB is currently the most comprehensive resource of NATs in the plant kingdom, which can serve as a reference database to investigate the regulatory function of NATs.

Proper citation: PlantNATsDB - Plant Natural Antisense Transcripts DataBase (RRID:SCR_013278) Copy   

•   Source: SciCrunch Registry

http://compbio.cs.ucr.edu/brat/

BRAT is an accurate and efficient tool for mapping short bisulfite-treated reads obtained from the Solexa-Illumina Genome Analyzer.

Proper citation: BRAT (RRID:SCR_013159) Copy   

•   Source: SciCrunch Registry

https://wiki.zfin.org/display/prot/ZFIN+Protocol+Wiki

ZFIN Protocol Wiki is where zebrafish researchers can share experimental protocols and tips with the rest of the research community. Protocols are organized into sections corresponding to the chapters of The Zebrafish Book, 5th edition (4th edition on-line). Feel free to add new protocols to the appropriate section or add comments to any existing protocol. Sections * General Methods for Zebrafish Care * Breeding * Embryonic and Larval Culture * Imaging * Cellular Methods * Dissociated Cell Culture * Genetic Methods * Antisense Methods * Histological Methods * in situ Hybridization Techniques * Mapping * Transgenesis * Gene Cloning * DNA Analysis * RNA Analysis * Protein Analysis * Microarray * Recipes

Proper citation: ZFIN Protocol Wiki (RRID:SCR_013239) Copy   

•   Source: SciCrunch Registry

http://alumni.cs.ucr.edu/~liw/cem.html

An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.

Proper citation: CEM (RRID:SCR_013241) Copy   

•   Source: SciCrunch Registry

http://qccpack.sourceforge.net

QccPack provides an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack has been written to provide very flexible and general implementations of procedures commonly used in coding and compression applications. QccPack is intended for use in the development of prototypes of coding and compression systems, and in academic research. QccPack includes routines for entropy coding, scalar quantization, vector quantization, and wavelet transforms. Additonally, an open-source implementation of SPIHT is available as an optional module. QccPack provides an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack has been written to provide very flexible and general implementations of procedures commonly used in coding and compression applications. The essential component of the QccPack collection is a library (a static library, libQccPack.a, and, if supported on your system, a dynamic library, libQccPack.so) of procedures implementing a large variety of compression and coding algorithms. Application programs may make use of the QccPack library routines by linking the application against the library during compilation. Each library function is very general in its implementation so to be useful in a large variety of applications. Additionally, much of the functionality of the library routines has been provided in the form of stand-alone executable programs. Probably the prime importance of these utility programs is that they provide examples of how to interface with many of the QccPack library routines. The utility programs could also be called from scripts to simulate the operation of complex coding and compression systems before implementing all the system functionality into one stand-alone program. Currently, QccPack consists of over 55,000 lines of C code implementing over 500 library routines and over 50 stand-alone utility programs. The major functionalities currently implemented include: * Entropy coding o Arithmetic coding including multiple-context adaptive and nonadaptive models o Huffman coding o Golomb and adaptive Golomb coding * Scalar Quantization (SQ) o Uniform SQ o Dead-zone SQ o -law and A-law SQ o Lloyd algorithm for optimal SQ design * Vector quantization (VQ) o Generalized Lloyd algorithm (GLA) for VQ-codebook design o Full-search VQ encoding and decoding o Entropy-constrained-VQ (ECVQ) training, encoding, and decoding o Multistage VQ (MSVQ) (also called residual VQ (RVQ)) training, encoding, and decoding * Adaptive vector quantization (AVQ) o The generalized-threshold-replenishment (GTR) algorithm o The Paul algorithm o Gersho-Yano algorithm o Coding of side information * Wavelet transforms, wavelet-based subband coding o Discrete wavelet transform (DWT) using first-generation filter banks and popular orthonormal and biorthogonal wavelets o Lifting implementations of DWT for popular wavelets o Two-dimensional DWT in the form of dyadic subband pyramids o Three-dimensional DWT in the form of dyadic subband pyramids as well as a packet transform o Shape-adaptive DWT (SA-DWT) for 1D and 2D signals o Redundant DWT (RDWT), aka, the algorithme trous o The SR algorithm for wavelet-based image coding o The SFQ algorithm for wavelet-based image coding o The WDR algorithm for wavelet-based image coding o The 3D-WDR algorithm for wavelet-based image-cube coding o The tarp-filter algorithm for wavelet-based image coding o The 3D-tarp algorithm for wavelet-based image-cube coding o The TCE algorithm for wavelet-based image coding o The BISK algorithm for wavelet-based shape-adaptive image coding o The 3D-BISK algorithm for wavelet-based image-cube coding * Error-correcting codes o Field arithmetic, including Gaussian-elimination matrix inversion o Reed-Solomon encoding and decoding o CRC codes o Trellis codes o Hard and soft Viterbi decoding * Image processing o Routines for reading and writing gray and color still images and sequences of images (via PGM and PPM formats) o Routines for reading and writing 3D image-cube volumes o Image and image-sequence deinterlacing o Image differential-pulse-code modulation (DPCM) o Color-space conversions: RGB, YUV, CIE XYZ, CIE UCS, CIE modified UCS o Block-based DCT and inverse DCT * Video coding o The spatial-block algorithm for image-sequence coding o The RDWT-block algorithm for image-sequence coding o The RWMH algorithm for image-sequence coding o Block-based motion estimation and motion compensation o Motion estimation and motion compensation using regular triangle meshes o Encoding and decoding of motion-vector fields * General routines o Vector math (up/down sampling, sorting, dot product, addition/subtraction, etc.) o Matrix math (addition/subtraction, vector-matrix multiplication, etc.) o Linked lists and associated operations o Entropy estimation (first and second order) o General file input and output, including automatic detection and reading/writing of gzip-compressed files o Character bit-packing for binary bitstream input/output o Memory-based fifo for binary bitstreams o Conversion between various file formats used by library routines o Error-message tracking, formatting, and output o Automatic command-line parameter parsing In addition to the standard functionalities listed above, there exist optional modules that can be added to the QccPack library. Usually, these modules are available under licensing terms different from the GPL/LGPL licenses of QccPack and may contain patented algorithms; refer to the documentation included with each module for specific details. These modules are downloaded separately from QccPack and are not enabled by default during the building of QccPack. The currently available optional modules and their functionalities are: * QccPackSPIHT o The Set Partitioning in Hierarchical Trees (SPIHT) algorithm for wavelet-based image coding * QccPackSPECK o The Set-Partitioning Embedded Block (SPECK) algorithm for wavelet-based image coding Abstract: We describe the QccPack software package, an open-source collection of library routines and utility programs for quantization, compression, and coding of data. QccPack is being written to expedite data-compression research and development by providing general and reliable implementations of common compression techniques. Functionality of the current release includes entropy coding, scalar quantization, vector quantization, adaptive vector quantization, wavelet transforms and subband coding, error-correcting codes, image-processing support, and general vector-math, matrix-math, file-I/O, and error-message routines. All QccPack functionality is accessible via library calls; additionally, many utility programs provide command-line access. The QccPack software package, downloadable free of charge from the QccPack Web page, is published under the terms of the GNU General Public License and the GNU Library General Public License which guarantee source-code access and as well as allow redistribution and modification. Additionally, there exist optional modules that implement certain patented algorithms. These modules are downloadable separately and are typically issued under licenses that permit only non-commercial use. This material is based upon work supported in part by the National Science Foundation under Grant No. INT-9600260.

Proper citation: QccPack (RRID:SCR_013240) Copy   

•   Source: SciCrunch Registry

http://mobyle.pasteur.fr/

A portal for bioinformatics analyses, including the following: alignment assembly database display genetics hmm information nucleic phylogeny protein sequence structure

Proper citation: Mobyle@Pasteur (RRID:SCR_013089) Copy   

•   Source: SciCrunch Registry

http://bioinfo.au.tsinghua.edu.cn/seqsite/

Software for detecting transcription factor binding sites from ChIP-seq data.

Proper citation: SeqSite (RRID:SCR_013243) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.9/bioc/html/Repitools.html

Software tools for the analysis of enrichment-based epigenomic data.

Proper citation: Repitools (RRID:SCR_013242) Copy   

•   Source: SciCrunch Registry