Curator Dashboard

Provides support for students, postdoctoral fellows, and faculty interested in the use of computational approaches to solving biological problems. Our goal is to lower as much as possible the threshold to enter the -omics area of the life sciences.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

A dataset of 100 annotated papers for use in text mining applications, that includes the importance of each reference compared to other references. Useful for natural language processing, machine learning or bibliometrics. To collect the annotations, authors of a paper were asked to determine whether a given reference had a strong influence on their research. In a blog post on March 20th 2012, authors were invited to help create a gold-standard dataset of labeled references. Data are available for download.

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• SciCrunch
• 14 years ago - by Anonymous

Core is dedicated to analysis of RNA and DNA sequence, structure and interactions in biological and biochemical processes.Specializes in Genomics, Metagenomics, Transcriptomics, Epigenomics, Interactomics, Oncogenomics, Structural Genomics and other fields. Equippment includes NovaSeq 6000, NextSeq 500 and MiSeq next generation sequencing systems and instruments for fractionation, quality and quantity assessment. Services include consultation and assistance, preparation of libraries from DNA (WGS, WES, Amp-seq, ATAC-Seq, ChIP-seq etc.) and RNA (different fractions: mRNA-seq, mRNA-seq, total RNA-seq, miRNA-seq, RIP-seq etc.), sequence custom libraries and conduct bioinformatic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

A Java applet tool for DT-MRI processing. It opens Diffusion-Weighted MRI datasets from user's computer and performs very efficient tensor field estimation using parallel threaded processing on user's browser. No installation is required. It runs on any operating system that supports Java (Windows, Mac, Linux,...). The estimated tensor field is guaranteed to be positive definite second order or higher order and is saved in user's local disc. MATLAB functions are also provided to open the tensor fields for your convenience in case you need to perform further processing. The fanDTasia Java applet provides also vector field visualization for 2nd and 4th-order tensors, as well as calculation of various anisotropic maps. Another useful feature is 3D fiber tracking (DTI-based) which is also shown using 3d graphics on the user's browser.

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• SciCrunch
• 14 years ago - by Anonymous

Provides access to tools for imaging with short lived radionuclides, data analysis and is integrated with campus centers SARIC and nuclear medicine clinic for quantitative imaging of these tracers in vivo that provides spatial and temporal data in order to improve our basic understanding of biochemical pathways, disease processes and help select personalized treatments that enhance clinical care. Highlights of our center include On-campus capacity to develop and produce radiopharmaceuticals to address specific research questions using in-vivo, real-time imaging;PET/CT, SPECT/CT (and soon PET/MRI) imaging capability to quantify organ perfusion, assess metabolic pathways, receptor function and density, and measure pharmacodynamics.Applications are directed toward range of models, ranging from small animals to non-human primates, to humans.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Software package as multiple sequence alignment tool that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. Accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/Clustal, GCG/MSF, RSF.

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• SciCrunch
• 14 years ago - by Anonymous

Facility comprises Next Generation Sequencing, Single Cell Technologies and Data Management teams. Offers professional project counseling, library preparation, and sequence production support for Max Delbruck Center for Molecular Medicine and Berlin Institute of Health at Charite institutes in Berlin.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 19, 2022. Command line version of multiple sequence alignment program Clustal for DNA or proteins. Alignment is progressive and considers sequence redundancy. No longer being maintained. Please consider using Clustal Omega instead which accepts nucleic acid or protein sequences in multiple sequence formats NBRF/PIR, EMBL/UniProt, Pearson (FASTA), GDE, ALN/ClustalW, GCG/MSF, RSF.

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• SciCrunch
• 17 years ago - by Anonymous

Software package to provide set of functions designed to make working with strings easy. Consistent wrappers for common string operations.

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• SciCrunch
• 4 years ago - by Anonymous

Ontology that defines hierarchical display of different rat strains as derived from parental strains. Ontology Browser allows to retrieve all genes, QTLs, strains and homologs annotated to particular term. Covers all types of biological pathways including altered and disease pathways, and to capture relationships between them within hierarchical structure. Five nodes of ontology include classic metabolic, regulatory, signaling, drug and disease pathways. Ontology allows for standardized annotation of rat. Serves as vehicle to connect between genes and ontology reports, between reports and interactive pathway diagrams, between pathways that directly connect to one another within diagram or between pathways that in some fashion are globally related in pathway suites and suite networks.

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• SciCrunch
• 13 years ago - by Anonymous

Provides advance clinical, translational and public health research at UNMC and in the community and region. Provides expertise in quantitative sciences, including biostatistics, epidemiology, and health services research, and coordinates collaborative design, planning, conduct, analysis and interpretation of laboratory, clinical, and public health research studies.Provides educational training opportunities for graduate students and educational opportunities for public health, clinical, and translational investigators.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Database of dermatology cases and browsable by diagnosis, category or body site with 12,176 images, 583 contributors and dermatology links. You may retrieve images using any diagnosis, disease category, body site, pigmentation, image contributor, patient age, image name, and/or key words. You are welcome submit images or to download images for lectures and other teaching purposes - or with permission for other uses. Additionally, you may search DermAtlas from your website. Add YOUR Link On the DermAtlas'''' Add a Link Page you can associate your link with as many diagnoses as you like. Case submission If you have a high quality image that you would like to submit to DermAtlas, submit the requested information, and upload the image. The data and image will automatically be sent to the editors for review. You will be notified within one week of submission of images. In order for an image to be considered for inclusion into this collection, consent must be obtained from the patient or his/her legal guardian. Contributors are solely responsible for obtaining consent.

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• SciCrunch
• 17 years ago - by Anonymous

Connects industry members with Penn State research community of artificial intelligence and machine learning researchers and their students to solve real world problems and seize market opportunities.

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• SciCrunch
• 4 years ago - submitted by Gretta Kellogg

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for clustering biological sequences with many applications in various fields such as making non-redundant databases, finding duplicates, identifying protein families, filtering sequence errors and improving sequence assembly etc. It is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset. The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU and over a dozen scripts. * CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold. * CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold. * CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads. * CD-HIT-OTU cluster rRNA tags into OTUs The usage of other programs and scripts can be found in CD-HIT user''s guide. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik''s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 15 years ago - by Anonymous

Provides advanced electron imaging tools covering scale range from tens of micrometers to angstroms, and delivering valuable structural information for cell biology, microbiology, biomolecular, molecular, and materials sciences.Offers all major electron microscopy modalities.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core facility that provides the following services: User-based microscopy service, Microscopy training service. The Imaging Core provides access to standard digital and laser scanning confocal microscopy, multiphoton microscopy, unbiased stereology, and automated confocal microscopy for large scale genome-wide screens. In addition, the Core has substantial capabilities in quantitative and three-dimensional volumetric image reconstruction.

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• SciCrunch
• 13 years ago - by Anonymous

Equipped with Thermo Scientific Orbitrap IQ-X Tribrid mass spectrometer(+UVPD)- Vanquish Horizon UHPLC system. Provides experience in quantifying diverse groups of metabolites in cells, culture medium, bodily fluid, animal tissue, exhaled breath condensate, etc., and performes stable isotope tracing experiments using 13C, 15N, and 2H-labeled substrates. Support hypothesis generating untargeted and hypothesis driven targeted metabolomics studies from experimental design stage through data acquisition, data analysis, and interpretation.

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• SciCrunch
• 4 years ago - submitted by Edyta Vieth

Core facility that provides the following services: Gene targeting service, Transgenics service. The Transgenic Core centralizes the production of genetically altered mice for MRRC investigators in a cost-effective and efficient manner. The Core also provides expert assistance in the additional areas required for generating genetically altered mice, including transgene and targeting construct production, and transgenic mouse colony management. Core personnel are available to train investigators in all of the techniques required for the generation of genetically modified mice.

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• SciCrunch
• 13 years ago - by Anonymous

Frontier (Ver 4.1) is used to estimate stochastic frontier models. Frontier Version 4.1 Resource URL https://scicrunch.org/resources/about/registry/SCR_022959 Description FRONTIER is used to obtain maximum likelihood estimates of the parameters of a variety of stochastic production and cost frontiers, and estimates of mean and individual technical or cost efficiencies. Defining Citation SCR_022958 Community resources Status pending Submitter Email [email protected]

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• RRID
• 4 years ago - submitted by Carlos Alberto Zuniga Gonzalez

Core facility that provides the following services: Graphics services, All Research Related Photography.

Medical Arts Core DFCI offers complete services for Publications, Presentations and Advertising as follows: Custom/Computer Graphics illustrations, Design and Consulting full productions services, Photoshop training. Posters Productions/Brochure Printing on best selection of paper, canvas material and Backlit poster films. Lamination, LCD announcements creation and posting. Research Related Photography Equipment: * iMAC and PC computers * Posters printer * LCD electronic announcements TV units * Backlit Display units * Laminator * Scanner * Digital camera

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• SciCrunch
• 13 years ago - by Anonymous