Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. The SALTY study will contact approximately 25 000 twins born 1943 - 1958. One of the main purposes with the study is to continue to build up the Swedish Twin Biobank which was established by the Twin Gene project.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

The Graduate Program at the University of Michigan was constituted in 1971, making it the longest-standing neuroscience graduate program in the United States. We are a collegial and interactive group of 75 students and 115 faculty that perform research across the breadth of the neuroscience field. Neuroscience graduate students on this campus form a cohesive group, which promotes interactions among the faculty, making the Graduate Program the nexus of the neuroscience community. Graduates receive a Ph.D. in Neuroscience, which provides tremendous flexibility in choosing one's career path. There are more than 100 alumni of our Program, and these graduates work in academic research, industrial research and development, academic medicine and biotechnology. Our program captures the excitement and interaction intrinsic to the field of neuroscience. Students can seek admission to the Neuroscience Program by three different routes direct application to the Neuroscience Program, application via the Program in Biomedical Sciences and application via the Medical Scientist Training Program.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. FaceBase Biorepository is now collecting biological samples from people with cleft lip/palate and their family members. Information for Prospective Cases: Clefts of the lip and/or palate can be caused by a wide range of genetic, environmental and other factors. The FaceBase Biorepository will serve as a common source of both biological samples and information that can be made available to investigators trying to determine the underlying cause of these common birth defects. Genetic studies, in particular, will benefit from both family history information and having samples from affected individuals as well as their family members. DNA is the information containing molecules found in all the cells of our body and can be easily obtained from material such as blood or saliva samples. As part of the FaceBase Biorepository, we are requesting families to submit biological samples from specific family members as well as information from other family members that might be affected with either the same condition or a similar condition. The medical and family history information that is collected includes other relevant information such as exposure to possible environmental causes during pregnancy. The biorepository is managed by Nichole Nidey, a research study coordinator, and Jeff Murray, a pediatric clinical geneticist and researcher. They are available to speak with family members regarding questions they may have, including providing information about the biorepository and making arrangements for the collection of samples for those who wish to participate. All participation is voluntary. Your name or other personally identifiable information (name, address, etc) will be removed before information is placed in the biorepository. Summary data to show how the database itself has been used overall as well as updates on whether specific findings might have been made using this database will be available on the FaceBase website at www.facebase.org. A newsletter containing this information will also be given to families and referring clinicians so that they may discuss the specifics with the families if there appears to be information that might be relevant in a particular case. Families will also need to sign a consent form that has been approved by the Institutional Review Board at the University of Iowa. Also, any submitted samples or data can also be removed from the database at any time should the family no longer wish to participate. Investigators interested in requesting DNA samples or for more information, please contact cleftresearch (at) uiowa.edu, Nichole Nidey, nichole-nidey (at) uiowa.edu or (319) 353-4365, or Jeff Murray, jeff-murray (at) uiowa.edu.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision.

• Resource
• SciCrunch
• 12 years ago - by Anonymous

To satisfy the need for standardized terminologies several ontologies, we are developing the Ontology of Craniofacial Development and Malformation. When complete, this ontology will describe several realms of anatomy and development relevant to FaceBase, including: * Human craniofacial anatomy, including developmental progressions * Craniofacial malformations * Mouse craniofacial anatomy * Mappings between mouse and human anatomy These ontologies are currently undergoing active development. As a result, these files should be considered very preliminary. They may not work correctly, and contents will almost certainly undergo significant change. Five (sub) ontologies in this zip archive correspond to the categories described above. * OCDM - Ontology of Craniofacial Development and Malformation: currently imports the CHO, CMO, and the CHMMO. * CHO - Craniofacial Human Ontoloogy: normal adult human craniofacial anatomy derived from the FMA. * CMO - Craniofacial Mouse Ontology: normal adult mouse craniofacial anatomy * CHMMO - Craniofacial Human-Mouse Mapping Ontology: mappings of classes in the * CHO to related (homologous) structures in the CMO. CFMO - Craniofacial Malformation Ontology: abnormal human anatomy, includes the CHO All ontologies are in Protege Frames format (requires Protege 3.x). Ontologies refer to other ontologies via the Protege include mechanism. The CHMMO includes the CHO and the CMO. The OCDM (which is the umbrella ontology) includes all of the rest. Future releases will include translations to the OWL language.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

A web portal that provides access to data, tools and materials that will aid in craniofacial research. Included is access to genomic and imaging based data sets from a variety of species, including zebrafish, human and mouse.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Tool box for arterial spin labeled perfusion MRI data processing. It is based on SPM and Matlab. More detailed documentation can be found in asl_perf_subtract.m, the main function for calculating CBF value. It supports 3D or 4D Analyze or Nifiti format and PASL, CASL, and PCASL data. It contains the code for calculating CBF and a set of SPM batch scripts for preprocessing and statistical analysis.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

A software package for automatic segmentation of hippocampal subfields in magnetic resonance imges. Given a pair of T1-weighted and T2-weighted images (the latter acquired using a protocol tuned for hippocampus imaging), ASHS will automatically label main subfields of the hippocampus, and some extra-hippocampal structures, using multi-atlas segmentation. The main method is described in the Yushkevich et al. 2011 Neuroimage paper (http://tinyurl.com/cffrp3p). * execution requires: Advanced Normalization Tools, FSL

• Resource
• SciCrunch
• 15 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A probabilistic algorithm that addresses the computational problems associated with aligning bisulfite sequencing data to a reference genome.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Toolbox for post-processing fMRI data. Includes software for comprehensive analysis of sources of artifacts in timeseries data including spiking and motion. Most compatible with SPM processing, but adaptable for FSL as well. * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE

• Resource
• SciCrunch
• 15 years ago - by Anonymous

ART ''''acpcdetect'''' program for automatic detection of the AC and PC landmarks and the mid-sagittal plane on 3D structural MRI scans. ART ''''brainwash'''' program for automatic multi-atlas skull-stripping of 3D structural MRI scans. ART ''''3dwarper'''' program of non-linear inter-subject registration of 3D structural MRI scans. Software (art2) for linear rigid-body intra-subject inter-modality (MRI-PET) image registration. Data resource: The ART projects makes available corpus callosum segmentations of 316 normal subjects from the OASIS cross-sectional database. ART ''''yuki'''' program for fast, robust, and fully automatic segmentation of the corpus callosum on 3D structural MRI scans.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Ontology specifically for Randomized Controlled Trials in order to facilitate the production of systematic reviews and metaanalysis.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Database of high-quality craniofacial anthropometric normative data for the research and clinical community based on digital stereophotogrammetry. Unlike traditional craniofacial normative datasets that are limited to measures obtained with handheld calipers and tape measurers, the anthropometric data provided here are based on digital stereophotogrammetry, a method of 3D surface imaging ideally suited for capturing human facial surface morphology. Also unlike more traditional normative craniofacial resources, the 3D Facial Norms Database allows users to interact with data via an intuitive graphical interface and - given proper credentials - gain access to individual-level data, allowing users to perform their own analyses.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

A toolbox for SPM to improve fMRI analysis of high motion pediatric and clinical subjects. The toolbox includes special algorithms for motion adjustment, data repair, and noise filtering, and methods to find outlier subjects in group studies. Visualization tools are included for quality checking the data, including a movie format for viewing all data and all contrast estimates on every voxel of every subject. Methods are included to quantify results into percent signal change. * Operating System: OS Independent * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1 * execution requires: SPM

• Resource
• SciCrunch
• 15 years ago - by Anonymous

An end-to-end application allowing individual regional analysis of cortical thickness. This cross-platform tool can be run within Slicer3 as an external module, or directly as a command line. * Operating System: MacOS, Linux * Programming Language: C++ * Supported Data Format: ANALYZE, Nrrd, Other Format * build requires: Insight Toolkit

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Software toolkit for the visualization, segmentation, registration and analysis of multidimensional biomedical imaging data. With Analyze, both anatomic structure and associated function can be studied and fused together for synergistic display and measurement of important structure-to-function relationships.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A virus protein interactions database that collects and annotates all the interactions between human and viral proteins and integrates this information in the human protein interaction network. It uses the PSI-MI standard and is fully integrated with the MINT database. You can search for any viral or human protein by entering either common names or database identifiers or display a complete viral interactome.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A web-compliant application that allows connectomics visualization by converting datasets to web-optimized tiles, delivering volume transforms to client devices, and providing groups of users with connectome annotation tools and data simultaneously via conventional internet connections. Viking is an extensible tool for connectomics analysis and is generalizable to histomics applications.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

An Antibody supplier

• Resource
• SciCrunch
• 14 years ago - by Anonymous

API and demo application for accessing the Allen Brain Atlas Mouse Brain data. Data available via the API includes download high resolution images, expression data from a 3D volume, 3D coordinates of the Allen Reference Atlas, and searching genes with similar gene expression profiles using NeuroBlast. Data made available includes: * High resolution images for gene expression, connectivity, and histology experiments, as well as annotated atlas images * 3-D expression summaries registered to a reference space for the Mouse Brain and Developing Mouse Brain * Primary microarray results for the Human Brain and Non-Human Primate * RNA sequencing results for the Developing Human Brain * MRI and DTI files for Human Brain The API consists of the following resources: * RESTful model access * Image download service * 3-D expression summary download service * Differential expression search services * NeuroBlast correlative searches * Image-to-image synchronization service * Structure graph download service

• Resource
• SciCrunch
• 15 years ago - by Anonymous