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http://bcbio.wordpress.com/

This blog will appeal to those dealing with the practical day to day work of biological data analysis and presentation.

Proper citation: Blue Collar Bioinformatics (RRID:SCR_012913) Copy   

•   Source: SciCrunch Registry

http://tools.neb.com/NEBcutter2/

This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and submit. Further options will appear with the output. The maximum size of the input file is 1 MByte, and the maximum sequence length is 300 KBases. NEBcutter produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://rebase.neb.com/rebase/rebase.html). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini.

Proper citation: NEBcutter (RRID:SCR_010664) Copy   

•   Source: SciCrunch Registry

http://www.irantumorbank.com/

Not yet vetted by NIF curator

Proper citation: Iran National Tumor Bank (RRID:SCR_010666) Copy   

•   Source: SciCrunch Registry

http://www.ifti.org/cgi-bin/ifti/Tfsitescan.pl

The Tfsitescan tool is for promoter sequence analysis and works best with sequences of ~500 nt. Simply enter the nucleic acid sequence in one of the common sequence formats (IG, Genbank, EMBL, GCG, DNAStrider, or Fasta).

Proper citation: TfSiteScan (RRID:SCR_010667) Copy   

•   Source: SciCrunch Registry

http://www.asterand.com/

Provides human tissue for drug discovery scientists. * Human Biospecimens: Frozen & Fixed Human Tissues; Human RNA/DNA; Human Primary Cells / Cell lines; Custom Procurement; Oncology tissue, biofluid and RNA sets at special prices * Human Tissue-Based Services: Gene Expression, Molecular Pathology, Biochemical Pharmacology, Metabolism and Toxicity * Predictive Human Disease Models

Proper citation: Asterand (RRID:SCR_010703) Copy   

•   Source: SciCrunch Registry

http://www.benoslab.pitt.edu/comir/

Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data.

Proper citation: ComiR (RRID:SCR_013023) Copy   

•   Source: SciCrunch Registry

http://www.tissue-solutions.com/

Tissue Solutions offers you a single point to access the entire range of human biological materials for all your research and development needs. This includes diseased and normal tissues in fresh, frozen and FFPE formats. Using our large network of ethical sources we find the tissues you require, to your specifications and will deliver them to your door. Our goal is to provide high quality and well characterized samples to biotech companies, the pharmaceutical community and contract research organizations worldwide. We also organize customized and prospective tissue acquisition projects and give specialized advice relating to all aspects of the acquisition process, including intellectual input on project design. We appreciate that you would rather spend your time finding new biomarkers and developing, testing and validating novel drugs to cure human disease than spend your time sourcing material to help you do your work, so let our dedicated Tissue Acquisitionists lessen your workload and become a virtual part of your team.

Proper citation: Tissue Solutions (RRID:SCR_010672) Copy   

•   Source: SciCrunch Registry

http://trex.biohpc.org/

T-REX is a free, platform-independent online tool that allows for an integrated, rapid, and more robust analysis of T-RFLP data. Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that hamper the analysis of these datasets. Many steps are required to process raw data into a format ready for analysis and interpretation. These steps can be time-intensive, error-prone, and can introduce unwanted variability into the analysis. Accordingly, we developed T-REX, free, online software for the processing and analysis of T-RFLP data. Analysis of T-RFLP data generated from a multiple-factorial study was performed with T-REX. With this software, we were able to i) label raw data with attributes related to the experimental design of the samples, ii) determine a baseline threshold for identification of true peaks over noise, iii) align terminal restriction fragments (T-RFs) in all samples (i.e., bin T-RFs), iv) construct a two-way data matrix from labeled data and process the matrix in a variety of ways, v) produce several measures of data matrix complexity, including the distribution of variance between main and interaction effects and sample heterogeneity, and vi) analyze a data matrix with the additive main effects and multiplicative interaction (AMMI) model.

Proper citation: T-REX (RRID:SCR_010715) Copy   

•   Source: SciCrunch Registry

http://comet.gobics.de/

A web-server for fast comparative functional profiling of metagenomes.

Proper citation: CoMet (RRID:SCR_011925) Copy   

•   Source: SciCrunch Registry

http://eagle-i.itmat.upenn.edu/i/0000013f-52ff-7e24-a468-831a80000000

The MR Sub-Core of the SAIF provides the instrumentation and expertise necessary to perform a broad spectrum of magnetic resonance imaging and spectroscopy studies on a wide range of biological samples including small animals (cats, rabbits, rats, mice), tissue specimens, cultured cells and tissue extracts. This facility includes a conveniently located, well equipped surgery room used for preparing the animals for MR exams and a wide assortment of supporting equipment, i.e. anesthesia machines, MR compatible vital signs monitors (SA Instruments), infusion pumps (Harvard), heating pads, etc. A variety of perishable supplies used in animal preparation are provided by the facility.

Proper citation: Penn Small Animal Imaging Facility: MRI/MRS Sub-Core (RRID:SCR_010032) Copy   

•   Source: SciCrunch Registry

http://www.med.upenn.edu/gtp/vectorcore/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core whose main aim is to provide vector technology for preclinical studies and other basic research applications. Its services include rovision of AAV, adenoviral and lentiviral based vectors, consultation and advice in the design of custom vectors and in vector serotype/pseudotype selection, and design, cloning and production of plasmid DNA for the production of custom vectors.

Proper citation: University of Pennsylvania Center for Molecular Therapy for Cystic Fibrosis Vector Core Facility (RRID:SCR_010038) Copy   

•   Source: SciCrunch Registry

http://eagle-i.itmat.upenn.edu/i/00000138-7ce8-c10b-fbab-3b8480000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Core facility that provides the following services: Flow cytometry analysis service, Cell sorting and analysis service, Flow cytometer analyzer access, Introductory flow cytometry training, Advanced and customized flow cytometry training, Flow cytometry consultation service, FACSAria training, Flow cytometry data analysis, BSL2+ biohazardous human cell sorting, BSL2+ murine biohazardous cell sorting, BSL2+ murine cell sorting access, Non-infectious cell sorting access. The Flow Cytometry and Cell Sorting Resource Laboratory is currently recognized as one of the largest and most comprehensive flow cytometry laboratories in the US. In 2010 it was designated a laboratory of exceptional merit by the National Cancer Institute. Using state-of-the-art technology, the resource provides a broad array of, instrumentation, support, education and consultation to the research community at the University of Pennsylvania. A wide variety of cell sorting applications are supported, from high-speed multicolor (up to 14 colors) cell sorting to low-speed, large nozzle, improved viability sorting. Additionally, a wide variety of cell analysis services (up to 20 parameters) are offered, from traditional analog, easier to use tabletop analyzers to many-laser, many-color, high-speed, fully-digital modern instrumentation. Currently the facility offers 6 cell sorters and 19 analytical instruments. A very active training and consultation program is in place to support these activities. The Scientific Director, Dr. Jonni Moore, and the Technical Director, each have over 25 years experience in the field of cytomics. Researchers at the University of Pennsylvania are increasingly engaged in research projects that require 8-plus-parameter cell sorting of infectious cells and primary human tissues. Investigators using the Flow Cytometry and Cell Sorting Shared Resource have access to virtually any type of cytometric services required for a vast array of applications.

Proper citation: Penn Flow Cytometry and Cell Sorting Resource Laboratory (RRID:SCR_010011) Copy   

•   Source: SciCrunch Registry

http://uccaribe.eagle-i.net/i/00000135-c95d-a6f3-a272-8ee780000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 26,2026. Core facility that provides the following services: Research support, Research Training. The DMSRSU provides study design, data management, quality assurance, and statistical analysis support for UCC researchers. The DMSRSU has a strong infrastructure which includes the following subunits: Data Abstraction and Management; Data Entry; Quality Control; Data Analysis and Consultant; and Administrative and Computer Systems. Each of these subunits consists of experienced professionals readily available to assist researchers and to provide data management and statistical research support to investigators. In addition, the DMSRSU counts on a highly experienced and reliable consulting team.

Proper citation: UCC Data Management and Statistical Research Support Unit (RRID:SCR_010074) Copy   

•   Source: SciCrunch Registry

https://www.wistar.org/resources/proteomics-metabolomics-facility/

Core facility that provides the following services: In-gel protease digestion service, LC-MS/MS protein identification service, Gel/LC-MS/MS Comprehensive analysis of a subproteome or proteome, MudPIT (LC/LC-MS/MS) analyis?comprehensive analysis of a subproteome or proteome, Reverse phase microbore HPLC peptide mapping service, MALDI mass spectrometry, ESI of intact proteins, Post-translational modification identifications, Custom proteomics database creation, Custom proteomics data analysis, Proteomics methods development. The Wistar Proteomics Facility provides mass spectrometry (MS) and sequence analysis of proteins and peptides at maximum sensitivity using state-of-the-art instruments and methods. The most commonly used services are identifications of either purified proteins or complex protein mixtures, such as sub-proteomes or complete proteomes, using electrospray ionization tandem mass spectrometry (ESI MS/MS). Typically, either individual bands are excised from 1-D SDS gels, or the entire gel lane is analyzed by slicing it into uniform fractions followed by trypsin digestion and nanocapillary HPLC interfaced directly with hybrid ion trap mass spectrometry (Gel/LC-MS/MS). Data is analyzed and filtered to produce low false-positive rates. Several options are available for quantitatively comparing protein changes in related samples, and additional options will be implemented in the future. Complementary services include reverse-phase microbore HPLC peptide mapping with UV detection and mass measurements of intact peptides and proteins using MALDI MS or ESI MS. Posttranslational modification (PTM) analyses including identifications of specific modified residues also are provided, although investigators should recognize that in most cases these studies are quite complex and require substantial effort. These studies, as well as analyses of complex protein mixtures, usually require preparation of custom sequence databases and/or custom data analyses, which can be provided by the facility as needed.

Proper citation: Wistar Proteomics and Metabolomics Core Facility (RRID:SCR_010211) Copy   

•   Source: SciCrunch Registry

http://upr.eagle-i.net/i/0000012a-250b-efe2-43fb-601a80000000

These laboratories house large, relatively expensive research instruments, which are shared among the faculty, students and staff on campus.

Proper citation: UPR RCMI Program Shared Instrumentation Laboratories (RRID:SCR_010132) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/histology-core-facility-iu

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 30,2024. The Histology Core of the Department of Anatomy and Cell Biology at the Indiana University School of Medicine provides histological services for basic science (non-clinical) research. Both mineralized (plastic embedded) and soft tissue (paraffin embedded) specimens can be prepared.

Proper citation: Indiana University School of Medicine Histology Core Facility (RRID:SCR_011020) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/genomics-and-microarray-laboratory-dartmouth

The Genomics and Microarray Laboratory (DGML) is supported by the Norris Cotton Cancer Center. DGML is a core facility for investigators at Dartmouth College and Dartmouth Hitchcock Medical Center to provide genomics products and services at or below cost.

Proper citation: Dartmouth Genomics and Microarray Laboratory (RRID:SCR_012190) Copy   

•   Source: SciCrunch Registry

http://www.tulane.edu/

Tulane University of Louisiana is a private research university in New Orleans, Louisiana, United States. Founded as the Medical College of Louisiana in 1834 by a cohort of medical doctors, it became a comprehensive public university in the University of Louisiana in 1847

Proper citation: Tulane University; Louisiana; USA (RRID:SCR_011548) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/flow-cytometry-core-facility-utah

Serving 120+ investigators with a 5 laser high speed sorter and 3 benchtop analyzers with 13+ color capabilities, the Utah Flow Cytometry Core Facility has developed a paradigm to balance productivity with quality to minimize the cost per research project, keep overall costs contained, and provide the necessary scientific support. Central to this paradigm is a close working relationship with investigators to define their projects in the early stages of development to make optimal and efficient use of flow cytometry. In addition to high quality and well maintained instrumentation, success of this approach requires focused efforts in three major areas: 1) education of ALL users (faculty and staff) in the science and technology of flow cytometry, 2) active involvement in the scientific development of the project, 3) continuing education for core staff.

Proper citation: University of Utah Flow Cytometry Core Facility (RRID:SCR_012210) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/mq-biofocus-research-centre

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2024. We develop and apply new analytical, microscopic, molecular, multiplexed, cellular, tomographic and related technologies for biomedical diagnosis, suitable for live cells or tissues or whole body. These will enable significantly increased sensitivity, resolution, speed, accuracy, penetration, and photostability , combined with reduced toxicity and risks to health.

Proper citation: MQ BioFocus Research Centre (RRID:SCR_011072) Copy   

•   Source: SciCrunch Registry