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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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DNAWorks at Helix Systems Resource Report Resource Website 10+ mentions |
DNAWorks at Helix Systems (RRID:SCR_008470) | service resource | DNAWorks automates the design of oligonucleotides for gene synthesis by PCR-based methods. The availability of sequences of entire genomes has dramatically increased the number of protein targets, many of which will need to be overexpressed in cells other than the original source of DNA. Gene synthesis often provides a fast and economically efficient approach. The synthetic gene can be optimized for expression and constructed for easy mutational manipulation without regard to the parent genome. DNAWorks accesses a computer program that automates the design of oligonucleotides for gene synthesis. The website provides forms for simple input information, i.e. amino acid sequence of the target protein and melting temperature (needed for the gene assembly) of synthetic oligonucleotides. The program outputs a series of oligonucleotide sequences with codons optimized for expression in an organism of choice. Those oligonucleotides are characterized by highly homogeneous melting temperatures and a minimized tendency for hairpin formation. The approach presented here simplifies the production of proteins from a wide variety of organisms for genomics-based studies. | oligonucleotide, pcr, oligo primer |
is listed by: 3DVC has parent organization: National Cancer Institute has parent organization: National Cancer Institute |
Intramural AIDS Targeted Antiviral Program of the Office of the Director ; NIH |
PMID:12000848 | nif-0000-30422 | SCR_008470 | DNAWorks | 2026-02-14 02:01:39 | 37 | |||||||
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SeqPig Resource Report Resource Website 1+ mentions |
SeqPig (RRID:SCR_008548) | SeqPig | software resource | A software library for Apache Pig for the distributed analysis of large sequencing datasets on Hadoop clusters. | mapreduce/hadoop |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24149054 | OMICS_01226 | SCR_008548 | 2026-02-14 02:01:40 | 2 | ||||||||
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RMA Express Resource Report Resource Website 100+ mentions |
RMA Express (RRID:SCR_008549) | software resource | RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics. It does not require R nor is it dependent on any component of the BioConductor project. If focuses on processing 3'' IVT expression arrays, exon and WT gene arrays. What is RMA? RMA is the Robust Multichip Average. It consists of three steps: a background adjustment, quantile normalization (see the Bolstad et al reference) and finally summarization. Some references (currently published) for the RMA methodology are: Bolstad, B.M., Irizarry R. A., Astrand, M., and Speed, T.P. (2003), A Comparison of Normalization Methods for High Density Oligonucleotide Array Data Based on Bias and Variance. Bioinformatics 19(2):185-193 Supplemental information Rafael. A. Irizarry, Benjamin M. Bolstad, Francois Collin, Leslie M. Cope, Bridget Hobbs and Terence P. Speed (2003), Summaries of Affymetrix GeneChip probe level data Nucleic Acids Research 31(4):e15 Irizarry, RA, Hobbs, B, Collin, F, Beazer-Barclay, YD, Antonellis, KJ, Scherf, U, Speed, TP (2002) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data. Accepted for publication in Biostatistics. [Abstract, PDF, PS, Complementary Color Figures-PDF, Software] What do I need? You will need the appropriate CDF and CEL files for your dataset. For Exon and WT Gene arrays, the PGF and CLF should be used instead of the CDF file to build a CDFRME file. The process for doing this is explained in the user manual. Some pre-built CDFRME files are also available. CDFRME files HuEx_CDFRME.zip (95.9MB) HuGene_CDFRME.zip (5.5MB) MoEx_CDFRME.zip (79.6MB) MoGene_CDFRME.zip (6.3MB) RaEx_CDFRME.zip (48.4MB) RaGene_CDFRME.zip (5.7MB) Can I use affy/BioConductor instead? Of course. Hypothetically you will get the same results from both places, provided you have consistent settings in affy/BioConductor and RMAExpress. Some people prefer the power and flexibility of R and others like the point and click simplicity of a GUI. RMAExpress caters to the second option. Since RMAExpress outputs the computed expression values to a text file, you may of course load the expression measures into R and use features of Bioconductor for the analysis of your gene expression values. You can of course open the results file in any other application that supports importing plain text files. Will I get the same results as I would using affy/Bioconductor? Yes. The results from RMAExpress should be consistent. What are the machine requirements? A good rule of thumb is the more RAM you have the better. I would recommend at least 1GB, though 512MB will work in most situations. At this point the program has been tested using Windows 2000, Windows XP, Windows Vista and Linux. Most recently I have had a report of over 10,000 arrays processed in a single session. Can I do any quality assessment? Yes, store the residuals when you compute the expression values. Then you may examine chip pseudo-images of the residuals. Note that high positive residuals are colored increasingly read and low negative residuals are colored increasingly blue. To better interpret these images and gain a better feel for what is typical you may visit the PLM Image Gallery where images for a number of different datasets are shown. Access to the NUSE and RLE quality assessment metrics is also provided. How do I download and install it? Click here for the current release Windows version. Use the installer to install the program. The current release version number is 1.0 (released June 29, 2008). A pre-built linux version is not currently available, but you may build it using the source code. You can download pre-release versions from the following table (the release versions will be more stable, the development versions may have features that are incomplete or will be removed or altered before the next release was supported by the PGA U01 HL66583. | nif-0000-31409 | SCR_008549 | RMAX | 2026-02-14 02:01:43 | 100 | |||||||||||
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Bionformatics Research Center Resource Report Resource Website 10+ mentions |
Bionformatics Research Center (RRID:SCR_008540) | BRC | software resource | QTL Cartographer is a suite of programs to map quantitative traits using a map of molecular markers. The programs are available via an anonymous ftp server. See the README for more information. You will also want a copy of Gnuplot to display plots made by QTL Cartographer. Gnuplot is freely available on the web. Do a search to find the latest version for your operating system. Windows QTL Cartographer Windows QTL Cartographer is a user friendly version of QTL Cartographer. It has a GUI interface and runs under Microsoft Windows. Manual The manual for QTL Cartographer is written in LaTeX2e. An Adobe Portable document format (pdf) version is available with the distribution of the programs. Look in the doc/pdf folder for the manual.pdf file. This file can be printed or viewed using Acrobat Reader, available through the Adobe website. The manual has also been translated into html. It is available through the following link. Please note that the translator is not perfect: The pdf form of the manual is much more accurate. Specifically, latex2html failed to translate figure 2.4 and simply printed 2.3 twice. Man Pages In the UNIX world, it is comman to have man pages for programs. We have written such a set of man pages, and these are available with the UNIX distribution. The man pages are also a part of the manual.pdf file. Here is a list of the man pages. 1. Emap 2. Rmap 3. Rqtl 4. Rcross 5. Qstats 6. LRmapqtl 7. SRmapqtl 8. Zmapqtl 9. JZmapqtl 10. MImapqtl 11. MultiRegress 12. Prune 13. Preplot 14. Eqtl 15. QTLcart Perl scripts QTL Cartographer comes with some perl scripts to automate repetitive tasks and reformat output files. They are available in the doc/scripts subdirectory of the distribution. Here are the man pages that explain what the scripts can do. 1. Bootstrap.pl is a script for running a bootstrap analysis. 2. CWTupdate.pl is used with Permute.pl for the comparison-wise thresholds. 3. EWThreshold.pl is used with Permute.pl for the experiment-wise thresholds. 4. GetMaxLR.pl is used with Permute.pl for the experiment-wise thresholds. 5. Model8.pl iterates Zmapqtl to find a stable set of cofactors for composite interval mapping. 6. Permute.pl is a script for running a permutation test. 7. Prepraw.pl allows you to reformat and check a Mapmaker data file. 8. SRcompare.pl will compare the set of cofactors in two SRmapqtl output files. 9. SSupdate.pl is used with Bootstrap.pl to update the sum and sum of squares for the likelihoods and parameter estimates. 10. Vert.pl converts text file line endings between Unix, Macintosh and Windows. 11. Ztrim.pl redisplays Zmapqtl output so that it fits in a terminal window. Data We are now posting published data sets to our web site. A list of links to the ftp subdirectories follows. Each directory contains a set of text files of data. Please read the Readme file in the directory for information on the data. 1. Zeng et al provide data for their paper Genetic architecture of a morphological shape difference between two Drosophila species. If you have any data that you would like to make available via our server, contact Chris Basten. Presentations From time to time, Chris Basten gives presentations on how to use QTL Cartographer. These presentations are created in Microsoft Powerpoint. The source file for the presentation is available with the distribution of the programs. Look in the doc subdirectory. Binary Traits See this for more information on the BTmapqtl module. This is an add-on written in LaurenMcIntyre''s lab. BTmapqtl is in the binary directory of the distribution (and is created with a make for the UNIX version). | has parent organization: North Carolina State University; North Carolina; USA | nif-0000-31386 | SCR_008540 | 2026-02-14 02:01:42 | 13 | ||||||||||
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CAT Resource Report Resource Website 10+ mentions |
CAT (RRID:SCR_008421) | CAT | software resource | A repository of tools for analysis and annotation of CAZYmes (Carbohydrate Active enZYmes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01676, biotools:CAt | https://bio.tools/CAT | SCR_008421 | 2026-02-14 02:01:38 | 13 | |||||||
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QIAGEN Resource Report Resource Website 10000+ mentions |
QIAGEN (RRID:SCR_008539) | commercial organization | A commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis. | is parent organization of: Ingenuity Pathways Knowledge Base | nif-0000-31384 | SCR_008539 | QIAGEN | 2026-02-14 02:01:36 | 85828 | ||||||||||
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Q-Value Software Resource Report Resource Website 1+ mentions |
Q-Value Software (RRID:SCR_008538) | software resource | Features: * This software takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. A point-and-click interface is now available! * The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. * A short tutorial on q-values and false discovery rates is provided with the manual. * Various plots are automatically generated, allowing one to make sensible significance cut-offs. * Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. * The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining. This research was supported in part by a National Science Foundation graduate research fellowship. | has parent organization: Stanford University; Stanford; California | nif-0000-31382 | SCR_008538 | Q-Value Software | 2026-02-14 02:01:43 | 5 | ||||||||||
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Apache Tomcat Resource Report Resource Website 1+ mentions |
Apache Tomcat (RRID:SCR_008411) | software resource | Apache Tomcat is an open source software implementation of the Java Servlet and JavaServer Pages technologies. The Java Servlet and JavaServer Pages specifications are developed under the Java Community Process. Apache Tomcat is developed in an open and participatory environment and released under the Apache License version 2. Apache Tomcat is intended to be a collaboration of the best-of-breed developers from around the world. We invite you to participate in this open development project. Apache Tomcat powers numerous large-scale, mission-critical web applications across a diverse range of industries and organizations. Some of these users and their stories are listed on the PoweredBy wiki page. | software, technology, application, java | Yahoo ; Microsoft ; Google ; Facebook ; HP ; Basis Technology ; Covalent ; IONA ; AirPlus International ; BlueNog ; Intuit ; Joost |
nif-0000-30114 | SCR_008411 | Apache Tomcat | 2026-02-14 02:01:42 | 7 | |||||||||
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GEDI Resource Report Resource Website 50+ mentions |
GEDI (RRID:SCR_008530) | GEDI | software resource | A program that opens a new perspective to the analysis of microarray data (e.g., gene expression profiling). Unlike traditional gene clustering software, GEDI is primarily sample-oriented rather than gene-oriented. By treating each high-dimensional sample, such as one microarray experiment, as an object, it accentuates the genome-wide response of a tissue or a patient and treats it as an integrated biological entity. Hence, GEDI honors the new spirit of a system-level approach in biology. Yet, it also allows the researcher to quickly zoom-in from global patterns onto individual genes that exhibit interesting expression behavior and retrieve gene-specific information. Therefore, GEDI unites a novel holistic perspective with the traditional gene-centered approach in molecular biology. GEDI allows experimental biologists or clinicians with no bioinformatics background to efficiently and intuitively navigate through a large number of expression profiles, each with a memorizable face, and inspect, group and collect them, like managing a stack of baseball cards. DYNAMIC ANALYSIS: The unique strength of GEDI, for which GEDI was originally developed, is that it can display the results of parallel monitoring of multiple high-dimensional time courses, such as the comparison of expression profile time evolution in response to a series of drugs. GEDI creates animated graphics showing how 10,000s of genes change their expression over time in response to 100s of separately tested drugs. STATIC ANAYLSIS: The signature graphical output of GEDI, the GEDI-mosaics provide a unique, one-glance visual engram that gives each microarray or other high-dimensional dataset a face. A characteristic of GEDI''s analysis is that it does not prejudicate any particular structure in the data (such as clusters or hierarchical organization). Thus, it allows the researcher to use human pattern recognition to perform a global first-level analysis of the data. Sponsor. The project was supported by the Air Force Office of Scientific Research and the National Health Institutes. It is distributed for free academic use by the Childrens Hospital, Boston., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30604 | SCR_008530 | The Gene Expression Dynamics Inspector, Gene Expression Dynamics Inspector | 2026-02-14 02:01:35 | 73 | |||||||||
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Wide Tag Resource Report Resource Website |
Wide Tag (RRID:SCR_008566) | software resource |
Headquartered in Redwood City California, WideTag is a pioneer in architecting computing systems that integrate sensors, positioning devices and memory with social, Web 2.0-style services in applications that revolutionize business and push consumer technology. |
nif-0000-31904 | http://www.openspime.com | SCR_008566 | Wide Tag | 2026-02-14 02:01:44 | 0 | ||||||||||
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Program DynaFit Resource Report Resource Website 100+ mentions |
Program DynaFit (RRID:SCR_008444) | software resource | Program DynaFit Analysis of (bio)chemical kinetics and equilibria Welcome to the DynaFit home page. Purpose Symbolic Notation Bibliographic Reference Numerical Methods Minimum System Requirements Purpose The main purpose of the program DynaFit is to perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data. The experimental data can be either initial reaction velocities in dependence on the concentration of varied species (e.g., inhibitor concentration vs. velocity), or the reaction progress curves (e.g., time vs. absorbance). Symbolic Notation The main advantage in using the program DynaFit is in the ability to characterize the (bio)chemical reacting system in terms of symbolic, or stoichiometric, equations. For example, the ``slow, tight'''' inhibition of a dissociative dimeric enzyme is described by the following text: Monomer Monomer <==> Enzyme : k1 k2 Enzyme Inhibitor <==> Complex : k3 k4 Enzyme Substrate <==> ReactiveX : k5 k6 ReactiveX --> Product Enzyme : k7 k8 The names of chemical species (Monomer, Enzyme, etc.) are entirely arbitrary and can be freely chosen by the investigator. Bibliographic Reference If you publish any results obtained by using DYNAFIT, plase cite the following reference: Kuzmic, P. (1996) Anal. Biochem. 237, 260-273. Program DYNAFIT for the Analysis of Enzyme Kinetic Data: Application to HIV Proteinase ABSTRACT A computer program with the code name DYNAFIT was developed for fitting either the initial velocities, or the time-course of enzyme reactions, to an arbitrary molecular mechanism represented symbolically by a set of chemical equations. Seven numerical tests and five graphical tests are applied to judge the goodness of fit. Experimental data on the inhibition of the dissociative dimeric proteinase from HIV were used in four test examples. A set of initial velocities was analyzed to see if a tight-binding inhibitor could bind to the HIV proteinase monomer. Three different sets of progress curves were analyzed (i) to determine the kinetic properties of an irreversible inhibitor; (ii) to investigate the dissociation and denaturation mechanism for the protease dimer; and (iii) to investigate the inhibition mechanism for a transient inhibitor. See a MEDLINE abstract with related references concerning the kinetics of HIV-1 protease. Numerical Methods The nonlinear regression module uses the Levenberg-Marquardt algorithm [1]. The time-course of (bio)chemical reactions is computed by the numerical integration of simultaous first-order ordinary differential equations, using the Livermore Solver of ODe Systems (LSODE, [2]). The composition of complex mixtures at equilibrium (e.g., in the concentration jump experiment where a complex mixture is incubated prior to the addition of a reagent) is computed by solving simultaneous nonlinear algebraic equations, namely, the mass balance equations for the component species, by using the multidimensional Newton-Raphson method [3]. References G. A. F. Seber and C. J. Wild (1989) Nonlinear Regression, Wiley, New York, p. 624. A. C. Hindmarsh (1983) ODEPACK: a systematized collection of ODE solvers; in Scientific Computing, ed. R. S. Stepleman et al., North Holland, Amsterdam, pp. 55--64. E. Kreyszig (1993) Advanced Engineering Mathematics; 7th ed., John Wiley, New York, p. 929. Minimum System Requirements DynaFit for Windows Intel Pentium III or Celeron class 800 MHz or faster processor Microsoft Windows XP (SP1) or 2000 (SP2) 128 MB RAM 20 MB Hard Disk Space Ethernet Network Interface Card required for license activation(1) CD/DVD-ROM drive required for software installation(2) (1) The Network Interface Card is used to compute a unique Computer ID, tied to a particular DynaFit license. Essentially the Computer ID required for license activation is an encrypted Media Access Control (MAC address) associated with the given Network Card. (2) CD/DVD-ROM is not required if the software is being installed by using the downloadable installer file dynafit-install.zip. Sponsor. This work has been supported by the NIH, grant No. R43 AI52587-02 and the U.S. Department of Defense, U.S. Army Medical Research and Materials Command, Ft. Detrick, MD, administered by the Pacific Telehealth & Technology Hui, Honolulu, HI, contract No. V549P-6073. | nif-0000-30477 | SCR_008444 | DynaFit | 2026-02-14 02:01:39 | 127 | |||||||||||
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Public Health Resources Unit Resource Report Resource Website 1+ mentions |
Public Health Resources Unit (RRID:SCR_008564) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. Tools were developed by the Critical Appraisal Skills Programme (CASP) to help with the process of critically appraising articles of the following types of research. These are available and free to download for personal use. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31450 | http://www.sph.nhs.uk/what-we-do/public-health-workforce/resources/critical-appraisals-skills-programme | http://www.phru.nhs.uk/Pages/PHD/resources.htm | SCR_008564 | PHRU | 2026-02-14 02:01:43 | 1 | ||||||||
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LAGAN Resource Report Resource Website 50+ mentions |
LAGAN (RRID:SCR_008558) | software resource | About the LAGAN Toolkit The LAGAN Tookit consists of four components: CHAOS CHAOS is a pairwise local aligner optimized for non-coding, and other poorly conserved regions of the genome. It uses both exact matching and degenerate seeds, and is able to find homology in the presence of gaps. LAGAN LAGAN is our highly parametrizable pairwise global alignment program. It takes local alignments generated by CHAOS as anchors, and limits the search area of the Needleman-Wunsch algorithm around these anchors; Multi-LAGAN Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment. M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic tree. Alignments are aligned to other alignments using the sum-of-pairs metric. Shuffle-LAGAN Shuffle-LAGAN is a novel glocal alignment algorithm that is able to find rearrangements (inversions, transpositions and some duplications) in a global alignment framework. It uses CHAOS local alignments to build a map of the rearrangements between the sequences, and LAGAN to align the regions of conserved synteny. The website uses scripts written by Alex Poliakov. The website was designed by Marina Sirota. | has parent organization: Stanford University; Stanford; California | DOI:10.1101/gr.926603 | OMICS_08469, nif-0000-31432 | https://sources.debian.org/src/lagan/ | SCR_008558 | LAGAN | 2026-02-14 02:01:42 | 82 | ||||||||
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SAFC Resource Report Resource Website 100+ mentions |
SAFC (RRID:SCR_008554) | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. A business division of Sigma-Aldrich Corporation, focusing on providing custom manufactured products and specialized services used in the industrial development and manufacturing, including processes, that bring new drugs and new electronic products to market., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31481 | SCR_008554 | SAFC | 2026-02-14 02:01:36 | 380 | ||||||||||
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Classifier Visualization in R Resource Report Resource Website 10+ mentions |
Classifier Visualization in R (RRID:SCR_008551) | software resource | ROCR is a package for evaluating and visualizing the performance of scoring classifiers in the statistical language R. It features over 25 performance measures that can be freely combined to create two-dimensional performance curves. Standard methods for investigating trade-offs between specific performance measures are available within a uniform framework, including receiver operating characteristic (ROC) graphs, precision/recall plots, lift charts and cost curves. ROCR integrates tightly with R''s powerful graphics capabilities, thus allowing for highly adjustable plots. Being equipped with only three commands and reasonable default values for optional parameters, ROCR combines flexibility with ease of usage. Performance measures that ROCR knows: Accuracy, error rate, true positive rate, false positive rate, true negative rate, false negative rate, sensitivity, specificity, recall, positive predictive value, negative predictive value, precision, fallout, miss, phi correlation coefficient, Matthews correlation coefficient, mutual information, chi square statistic, odds ratio, lift value, precision/recall F measure, ROC convex hull, area under the ROC curve, precision/recall break-even point, calibration error, mean cross-entropy, root mean squared error, SAR measure, expected cost, explicit cost. ROCR features: ROC curves, precision/recall plots, lift charts, cost curves, custom curves by freely selecting one performance measure for the x axis and one for the y axis, handling of data from cross-validation or bootstrapping, curve averaging (vertically, horizontally, or by threshold), standard error bars, box plots, curves that are color-coded by cutoff, printing threshold values on the curve, tight integration with Rs plotting facilities (making it easy to adjust plots or to combine multiple plots), fully customizable, easy to use (only 3 commands). ROCR can be used under the terms of the GNU General Public License. Running within R, it is platform-independent. | has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany | PMID:16096348 | nif-0000-31415 | SCR_008551 | ROCR: Classifier Visualization in R, ROCR | 2026-02-14 02:01:42 | 15 | |||||||||
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Cython C-Extensions for Python Resource Report Resource Website 100+ mentions |
Cython C-Extensions for Python (RRID:SCR_008466) | software resource | Cython is a language that makes writing C extensions for the Python language as easy as Python itself. Cython is based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. The Cython language is very close to the Python language, but Cython additionally supports calling C functions and declaring C types on variables and class attributes. This allows the compiler to generate very efficient C code from Cython code. This makes Cython the ideal language for wrapping external C libraries, and for fast C modules that speed up the execution of Python code. Sponsor. Google and Enthought funded Dag Seljebotn to greatly improve Cython integration with NumPy. Kurt Smith and Danilo Freitas were funded through the Google Summer of Code program to work on improved Fortran and C support respectively. |
is related to: Python Programming Language is required by: TomoMiner |
nif-0000-30401 | SCR_008466 | Cython | 2026-02-14 02:01:42 | 135 | ||||||||||
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Ultrasome Resource Report Resource Website |
Ultrasome (RRID:SCR_008465) | Ultrasome | software resource | An efficient methodology for detecting and delineating gains and losses of chromosomal material in DNA copy-number data. |
is listed by: OMICtools has parent organization: Broad Institute |
PMID:19228802 | Acknowledgement requested, Free for academic use | OMICS_00737 | SCR_008465 | 2026-02-14 02:01:39 | 0 | ||||||||
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D. rerio Blast Server Resource Report Resource Website 1+ mentions |
D. rerio Blast Server (RRID:SCR_008461) | service resource | This Blast server offers searches against all D. rerio finished and unfinished clones in the Sanger sequencing pipeline. You can now also search the de novo assemblies generated from sequencing of one doubled haploid homozygous individual of each the AB and Tuebingen strain. Both fish were sequenced to ~40x coverage using Illumina GA sequencing technology and the sequences were assembled using Phusion2, resulting in a 1,33 Gb AB and a 1.48 Gb Tuebingen assembly. Due to the short reads and short inserts and no integration of physical or genetic map data, both assemblies are highly fragmented - with an N50 contig size of about 5kb. Mis-assembly errors may also be present in the contigs. Please note these assemblies are independent additions to the assemblies released by the zebrafish genome project and are intended to aid identification of polymorphisms between these two strains. Charity. Genome Research Limited is a charity registered in England with number 1021457 | has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom | nif-0000-30406 | SCR_008461 | D. rerio | 2026-02-14 02:01:42 | 6 | ||||||||||
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Yahoo Developer Network Resource Report Resource Website 50+ mentions |
Yahoo Developer Network (RRID:SCR_008594) | software resource | The YUI Library is a set of utilities and controls, written with JavaScript and CSS, for building richly interactive web applications using techniques such as DOM scripting, DHTML and AJAX. YUI is available under a BSD license and is free for all uses. YUI is proven, scalable, fast, and robust. Built by frontend engineers at Yahoo! and contributors from around the world, it''s an industrial-strength JavaScript library for professionals who love JavaScript. | nif-0000-31921 | SCR_008594 | Yahoo | 2026-02-14 02:01:43 | 54 | |||||||||||
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WinLTP Resource Report Resource Website 100+ mentions |
WinLTP (RRID:SCR_008590) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Jan 16th 2025. WinLTP is a stimulation, data acquisition and on-line analysis electrophysiological software for studying Long-Term Potentiation (LTP), Long-term Depression (LTD), and related phenomena. WinLTP is multitasking and simultaneously runs 1) LTP stimulus/acquisition/analyzing sweeps with protocol scripting, and 2) continuous acquisition saving Axon Binary Files (abf). WinLTP runs on Windows PCI bus computers and uses National Instruments PCI M-Series boards and Axon Instruments'' Digidata 1320A and 1322A data acquisition boards. Other software that can use the M-Series boards includes Axograph Scientific''s AxoGraph X, WaveMetrics'' IGOR, National Instruments'' LabView, John Dempster''s Strathclyde Electrophysiology Suite (WinWCP and WinEDR), Silver lab''s Nclamp, and QUB data acquisition., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | has parent organization: University of Bristol; Bristol; United Kingdom | DOI:10.1016/j.jneumeth.2006.12.018 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-31907 | SCR_008590 | WinLTP | 2026-02-14 02:01:41 | 218 |
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