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http://www.asip.org/

The American Society for Investigative Pathology (ASIP) is a society of biomedical scientists who investigate mechanisms of disease. Investigative pathology is an integrative discipline that links the presentation of disease in the whole organism to its fundamental cellular and molecular mechanisms. It uses a variety of structural, functional, and genetic techniques and ultimately applies research findings to the diagnosis and treatment of diseases. ASIP advocates for the practice of investigative pathology and fosters the professional career development and education of its members. The mission of the Society is to promote the discovery, advancement, and dissemination of basic and translational knowledge in experimental pathology and related disciplines. This shall be achieved by fostering investigation into the pathogenesis, classification, diagnosis, and manifestations of disease through meetings, publications, and educational activities. ASIP welcomes basic and clinical biomedical research scientists as active members.

Proper citation: American Society for Investigative Pathology (RRID:SCR_005426) Copy   

•   Source: SciCrunch Registry

http://weizhong-lab.ucsd.edu/public/?q=softwares/cd-hit-454

A software program to identify artificial duplicates from raw 454 sequencing reads, including exact duplicates and near identical duplicates.

Proper citation: cd-hit-454 (RRID:SCR_005541) Copy   

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http://solexaqa.sourceforge.net/

Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology.

Proper citation: SolexaQA (RRID:SCR_005421) Copy   

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http://www.modelcrop.org/

A Brachypodium distachyon comparative genomics resource offering a genome browser, BLAST server, download capabilities, Brachypodium physical map, Comparative maps, and comparison with rice and Sorghum chromosomes. * Genome browser >>> Browse the v1.0 genome assembly and the v1.0 gene predictions from JGI/MIPS. Also displays JIC FST data (T-DNA lines) and alignments of ESTs from wheat, barley and Brachypodium. * BLAST server >>> BLAST your sequences against the Brachypodium sequence assembly and the predicted proteome. * Download sequence >>> Download sequence from the brachy assembly (limited to 50kb regions). Download complete assembly file as FASTA. Download sequence and additional data from the v1.0 annotated assemblyincluding protein-coding sequences as FASTA, translated coding sequences as FASTA, gene sequences as FASTA, and COS markers. PLEASE NOTE: The published genome analysis is based on the v1.0 annotation. The v1.2 annotation can be downloaded from MIPS. * Brachypodium physical map >>> Brachypodium physical map data displayed using SyMAP. (view in genome browser) * Comparative maps >>> Brachypodium genetic and physical maps aligned to rice and wheat. * Comparison with rice and Sorghum chromosomes >>> Dotplots of the Brachypodium assembly aligned to rice and Sorghum chromosomes.

Proper citation: modelcrop.org (RRID:SCR_005542) Copy   

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http://www.stress.org

The mission of AIS is to improve the health of the community by setting the standard of stress management in education, research, clinical care and the workplace. The American Institute of Stress educates medical practitioners, scientists, health care professionals and the public; conducts research; and provides information, training and techniques to prevent human illness related to stress.

Proper citation: American Institute of Stress (RRID:SCR_005419) Copy   

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http://nlmfoundation.org/

The primary mission of the Nancy Lurie Marks (NLM) Family Foundation is to help people with autism lead fulfilling and rewarding lives. The Foundation is committed to understanding autism from a scientific perspective, increasing opportunities and services available to the autism community and educating the public about autism. In pursuit of its mission, the Foundation develops and provides grants to programs in research, clinical care, policy, advocacy and education. Founded by Nancy Lurie Marks over 25 years ago, the NLM Family Foundation is one of the largest supporters of initiatives in these areas. The principal goal of the scientific program is to achieve a deeper understanding of the biological basis of autism, focusing on genetics, synaptic chemistry, the neurobiology of communication, systems biology and the physiology of movement. The Foundation funds peer-reviewed research, the development of collaborative investigator projects, and research fellowship programs. Through sponsorship of scientific conferences, symposia and workshops, the Foundation seeks to encourage innovation and provide a springboard to generate new avenues of shared inquiry. The NLM Family Foundation supports programs which focus on novel ways to improve the communication and social abilities of those with autism. Other programs are designed to increase advocacy for legal rights and access to support services for persons with autism, and to increase community understanding and openness to inclusion through education and documentary films.

Proper citation: Nancy Lurie Marks Family Foundation (RRID:SCR_005455) Copy   

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http://dna.leeds.ac.uk/methylviewer/

A simple integrated software tool for handling MAP (methyltransferase accessibility protocol) and MAP-IT (MAP individual templates) footprinting projects. It can process sequence data (*.txt, *.ab1 and *.scf) derived from the use of up to four different DNA methyltransferases.

Proper citation: MethylViewer (RRID:SCR_005448) Copy   

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https://code.google.com/p/bisulfighter/

A software package for detecting methylated cytosines (mCs) and differentially methylated regions (DMRs) from bisulfite sequencing data.

Proper citation: Bisulfighter (RRID:SCR_005440) Copy   

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http://epigenome.usc.edu/publicationdata/bissnp2011/

A software package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol. It contains the following key features: * Call and summarize methylation of any cytosine context provided (CpG, CHH, CHG, GCH et.al.); * Work for single end and paired-end data; * Accurtae variant detection. Enable base quality recalibration and indel calling in bisulfite sequencing; * Based on Java map-reduce framework, allow multi-thread computing. Cross-platform; * Allow multiple output format, detailed VCF files, CpG haplotype reads file for mono-allelic methylation analysis, simplified bedGraph, wig and bed format for visualization in UCSC genome broswer and IGV browser. BisSNP uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bis-SNP (RRID:SCR_005439) Copy   

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http://cushaw2.sourceforge.net/homepage.htm#latest

Software package for next-generation sequencing read alignment that is fast and parallel gapped read alignment to large genomes, such as the human genome.

Proper citation: CUSHAW (RRID:SCR_005479) Copy   

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http://eqtl.rc.fas.harvard.edu/idcheck/

Software that allows assessment of concordance between genotype (from SNP arrays or DNA sequencing) and gene expression (RNA-seq) samples. IDCheck compares the identity of RNA-seq reads and SNP genotypes using a likelihood based method. Based on maximum likelihood estimates of relevant parameters, we can detect sample contamination and identify correct sample pairs when swapping occurs.

Proper citation: IdCheck (RRID:SCR_005510) Copy   

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http://code.google.com/p/distmap/

A user-friendly software pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster. It is designed to be easily implemented by researchers who do not have expert knowledge of bioinformatics. As it does not have any dependencies, it provides full flexibility and control to the user. The user can use any version of a compatible mapper and any reference genome assembly. There is no need to maintain the mapper, reference or DistMap source code on each of the slaves (nodes) in the Hadoop cluster, making maintenance extremely easy.

Proper citation: DistMap (RRID:SCR_005473) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/project-stampy

A software package for the mapping of short reads from illumina sequencing machines onto a reference genome. It''s recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features: * Maps single, paired-end and mate pair Illumina reads to a reference genome * Fast: about 20 Gbase per hour in hybrid mode (using BWA) * Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome * High sensitivity for indels and divergent reads, up to 10-15% * Low mapping bias for reads with SNPs * Well calibrated mapping quality scores * Input: Fastq and Fasta; gzipped or plain * Output: SAM, Maq''s map file * Optionally calculates per-base alignment posteriors * Optionally processes part of the input * Handles reads of up to 4500 bases

Proper citation: Stampy (RRID:SCR_005504) Copy   

•   Source: SciCrunch Registry

http://snap.cs.berkeley.edu/

A sequence aligner software program that is 10-100x faster and simultaneously more accurate than existing tools like BWA, Bowtie2 and SOAP2. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools. This gives SNAP up to 2x lower error rates than existing tools and lets it match larger mutations that they may miss. SNAP also natively reads BAM, FASTQ, or gzipped FASTQ, and natively writes SAM or BAM, with built-in sorting, duplicate marking, and BAM indexing.

Proper citation: Scalable Nucleotide Alignment Program (RRID:SCR_005501) Copy   

•   Source: SciCrunch Registry

https://github.com/richardmleggett/nextclip/

A software tool for analysing reads from Long Mate Pair (LMP) libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads.

Proper citation: NextClip (RRID:SCR_005465) Copy   

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http://www.nipgr.res.in/ngsqctoolkit.html

A software toolkit for the quality control (QC) of next generation sequencing (NGS) data. The toolkit comprises of user-friendly stand alone tools for quality control of the sequence data generated using Illumina and Roche 454 platforms with detailed results in the form of tables and graphs, and filtering of high-quality sequence data. It also includes few other tools, which are helpful in NGS data quality control and analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NGS QC Toolkit (RRID:SCR_005461) Copy   

•   Source: SciCrunch Registry

http://mta.hu/english/

The Hungarian Academy of Sciences is the most important and prestigious learned society of Hungary. Its seat is at the bank of the Danube in Budapest, between Széchenyi rakpart and Akadémia utca.

Proper citation: Hungarian Academy of Sciences; Budapest; Hungary (RRID:SCR_005654) Copy   

•   Source: SciCrunch Registry

http://neuromorphometrics.com

Neuromorphometrics provides brain labeling and measurement services. Given raw MRI brain scans, we make precise quantitative measurements of the volume, shape, and location of specific neuroanatomical structures. Web tool for brain measurement services. Used for modeling living human brain and make quantitative measurements of volume, shape, and location of specific neuroanatomical structures using given MRI brain scans. Automated analyses are manually guided, inspected and certified by a neuroanatomical expert. Resource of neuroanatomically labeled MRI brain scans database. Resource for neuroanatomical localization and identification: NeuAtlas.

Proper citation: Neuromorphometrics (RRID:SCR_005656) Copy   

•   Source: SciCrunch Registry

http://www.phrap.org/consed/consed.html

A graphical tool for sequence finishing (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)

Proper citation: Consed (RRID:SCR_005650) Copy   

•   Source: SciCrunch Registry

http://www.chemnavigator.com/cnc/services/SCSORS_Overview.asp

ChemNavigator has extended its agreement with NCI to include the development of a new Semi-Custom Synthesis On-line Request System (SCSORS), funded mostly by NCI with additional financial support from the NIH Chemical Genomics Center (NCGC). The new SCSORS project will provide the NIH access to the world''s supply of synthetic chemistry available for drug discovery. Once fully formed, SCSORS will provide a strategy for all NIH scientists to circulate requests for specific chemical samples among thousands, if not tens of thousands, of synthetic chemists at suppliers registered in the system. Sample quantities will range from milligram up to kilogram scale requests. Suppliers will be provided tools that allow them to review these requests and make proposals to NIH scientists for the synthesis of substances. It is expected that using the SCSORS strategy will allow the NIH to acquire chemical samples at less than 10% of the internal cost of synthesis while offering access to world wide chemical expertise and diversity. Once fully implemented, SCSORS will become an archive of commercially accessible custom chemistry products for pharmaceutical research. It is expected that this database of commercially accessible substances will grow to over 250 million substances in the coming two years.

Proper citation: SCSORS - Semi-Custom Synthesis On-line Request System (RRID:SCR_005636) Copy   

•   Source: SciCrunch Registry