Curator Dashboard

The MAKER Web Annotation Service (MWAS) is an easily configurable web-accessible genome annotation pipeline. It''''s purpose is to allow research groups with small to intermediate amounts of eukaryotic and prokaryotic genome sequence (i.e. BAC clones, small whole genomes, preliminary sequencing data, etc.) to independently annotate and analyze their data and produce output that can be loaded into a genome database. MWAS is build on the stand alone genome annotation pipeline MAKER, and users who wish to annotate larger datasets and whole genomes are free to download MAKER for use on their own systems. MWAS identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MWAS can also automatically train popular gene prediction algorithms for use on new genomes for which pre-existing information is limited. MAKER is a member of the Generic Model Organism Database (GMOD) project and output produced by this site can be directly used with other GMOD tools. Annotations can be directly viewed online by the user via GBrowse, JBrowse, and Apollo, or they can be downloaded for local analysis and integration into a genome database. MWAS also supplies summary statistics on sequence features via the Sequence Ontology tool SOBA. MWAS should prove especially useful for emerging model organism genome projects with minimal bioinformatics expertise and computer resources, since a user can produce final genome annotations without having to install and configure any software locally.

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• SciCrunch
• 15 years ago - by Anonymous

Software tool to calculate fraction of shared bound peptides between HLA proteins. Command-line tool to calculate fraction of shared bound peptides between HLA alleles from NetMHCpan binding predictions. Compares fraction shared between HLA allele and individual taking into account HLA and KIR genotypes.

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• SciCrunch
• 7 years ago - by Anonymous

Core provides flow cytometry services. Staff members will help with experimental design, instrument training, sample acquisition, data analysis with software provided, and conventional/spectral cell sorting.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

Global biobanking organization that creates opportunities for networking, education, and innovation. ISBER provides a community for harmonizing approaches to emerging challenges in repositories, as well as fostering ideas to create new solutions.

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• SciCrunch
• 15 years ago - by Anonymous

Core provides scientific consultation, training and access to shared biophysical equipment for characterization and analysis of macromolecules and their complexes. Facility includes instruments measuring molecular interactions and assessing protein quality by Isothermal Titration Calorimetry (ITC), Surface Plasmon Resonance (SPR), Biolayer Interferometry (BLI), MicroScale Thermophoresis (MST), Differential Scanning Fluorimetry (DSF), Circular Dichroism (CD), Analytical Size Exclusion Chromatography with Multi-Angle Light Scattering (SEC-MALS), and Dynamic Light Scattering (DLS).

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Fully-staffed, open access nanofabrication lab provides services including Lithography, Etch (Dry/Wet), Deposition and Characterization.

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• RRID
• 1 year ago - by Anonymous

From time to time the Editor of Health and Stress interviews leaders in the field of stress management on a variety of topics for inclusion in our publications. Some interviews are listed below. For a complete list of interviews and content, you must be a member of AIS and access the Archives.

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• SciCrunch
• 15 years ago - by Anonymous

Assists researchers and clinicians with molecular and morphologic characterization of normal and disease tissues of interest in support of biomarker discovery and translational research. Offers both routine and advanced histology immunohistochemistry, in situ and whole slide scanning services.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Provides full-service consultation, sample processing and results. After running your samples, we will process your data using Mestranova and give you access to the raw data via email or Dropbox.

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• RRID
• 1 year ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.

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• RRID-Legacy
• 7 years ago - by Anonymous

EMAL is part of University of Michigan’s School of Earth and Environmental Sciences. Houses CAMECA SX100 electron microprobes, Rigaku X-ray diffractometers, and JEOL JSM-7800FLV field-emission scanning electron microscope. These instruments are used by researchers for chemical and structural characterization of solid materials.

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• RRID
• 1 year ago - submitted by Edyta Vieth

A suite of software that allow users to capture, manage, and analyze effectively data from DNA microarray experiments. The suite of tools consist of four major applications, Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis System (MIDAS), and Multiexperiment Viewer (MeV), as well as a Minimal Information About a Microarray Experiment (MIAME)-compliant MySQL database, all of which are freely available to the scientific research community.

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• SciCrunch
• 13 years ago - by Anonymous

Jupyter protocol implementation and client libraries. Part of Project Jupyter which exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages. Jupyter-client contains reference implementation of Jupyter protocol and provides client and kernel management APIs for working with kernels.

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• RRID-Legacy
• 7 years ago - submitted by Anita Bandrowski

Islet Core provides consultative advice and equipment and services for isolation and study of pancreatic islet structure and function in support of diabetes-related research.

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• RRID
• 1 year ago - submitted by Edyta Vieth

By collecting and analyzing blood samples from Geisinger''s large patient population, MyCode will help unlock the mysteries of some of the most devastating and debilitating diseases. Blood samples are obtained from patients of certain Geisinger specialty clinics to study specific conditions, such as obesity and cardiovascular disease, and also from patients of Geisinger primary care clinics to provide a representative sample of the regional population. More than 60,000 samples from over 23,000 Geisinger patients have been collected so far, and sample collection is ongoing. MyCode researchers use the blood samples to study the genetic causes of diseases and certain disease-related molecular mediators. Knowledge gained from these studies will allow researchers to pursue innovative approaches to disease prevention, diagnosis and treatment. To be of value for Genomic Medicine research, bio-banked samples must be connected to clinical data: MyCode allows genetic and molecular data about the samples to be connected to medical data in a way that protects patient identity. When a patient agrees to participate in MyCode, blood samples for the MyCode Project are collected during blood draws ordered as part of the patient''s routine medical care. After the sample is drawn and labeled, a staff member from the Weis Center for Research transports the blood to the Geisinger Clinic Genomics Core (GCGC) where it is processed for storage. At this stage, all personal identification markers are removed and the samples are assigned a randomly-selected identification number. A secure key is maintained that allows approved researchers to connect the samples to the clinical data for genomic studies in a way that ensures confidentiality of the information. To maintain confidentiality of MyCode data the code linking the research numbers and the electronic health records are kept in a password-protected files accessible only to MyCode team members. Additionally, all results generated from the samples are reported as a group so that individuals are not identified. The samples are stored indefinitely.

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• SciCrunch
• 16 years ago - by Anonymous

Software suite that works by themselves, and with Amber20 itself. Can be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

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• SciCrunch
• 7 years ago - submitted by Nathan Anderson

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• RRID
• 1 year ago - submitted by Moira Sheehan

ToppGene Suite is a one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network. ToppGene Suite is a one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations. The similarity scores from individual features are combined into an overall score using statistical meta-analysis.

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• SciCrunch
• 15 years ago - by Anonymous

Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions.

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• RRID-Legacy
• 7 years ago - submitted by Nathan Anderson