Curator Dashboard

ooTFD (object-oriented Transcription Factors Database) is a successor to TFD, the original Transcription Factors Database. This database is aimed at capturing information regarding the polypeptide interactions which comprise and define the properties of transcription factors. ooTFD contains information about transcription factor binding sites, as well as composite relationships within transcription factors, which frequently occur as multisubunit proteins that form a complex interface to cellular processes outside the transcription machinery through protein-protein interactions. ooTFD contains information represented in TFD but also allows the representation of containment, composite, and interaction relationships between transcription factor polypeptides. It is designed to represent information about all transcription factors, both eukaryotic and prokaryotic, basal as well as regulatory factors, and multiprotein complexes as well as monomers.

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• SciCrunch
• 17 years ago - by Anonymous

Core that offers measurement of gut permeability, plasma lipopolysaccharide binding protein (LBP) assay, and inflammatory profiling.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Core for assisting with custom instrumentation and equipment needs at affordable price.Projects devices include microcontrollers, LCD displays, keypad interfaces, serial communication, signal conditioning electronics, analog and digital computer interfaces, photomultiplier tube amplifiers, DC motor, stepper motor and linear motor controllers, servomotors, rotary encoders, timed sequenced equipment, temperature controllers, peltier devices, solenoid valves, actuators, force transducers, profusion chambers, microscope adapters as well as mechanical design and limited machine shop services.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

An open source learning-based software that automatically learns how to transfer the output of a host segmentation tool closer to the user's manual segmentation using the image data and manual segmentation provided by the user. The motivation of this project is to bridge the gap between the segmentation tool developer and the tool users such that the existing segmentation tools can more effectively serve the community. More and more automatic segmentation tools are publicly available to today's researchers. However, when applied by their end-users, these segmentation tools usually can not achieve the performance that the tool developer reported. Discrepancies between the tool developer and its users in manual segmentation protocols and imaging modalities are the main reasons for such inconsistency.

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• SciCrunch
• 14 years ago - by Anonymous

Core that provides consultations for study design and analysis, preparation of grant applications, preparation of statistical methods and results for manuscripts on completed studies, responses to reviewer comments for manuscript resubmissions, identification of possible long term statistical collaborators for grants.

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• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Service core arm of Center for Neurocognition and Behavior. Used for measuring healthy human brain and behavior in action. Facility houses equipment, including MRI, SQUID and triaxial OPM MEG, EEG, NIRS, TMS, VR, eye-tracking, and body motion tracking.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Matlab script that uses the Pythagorean Theorem to calculate head motion and position, while preserving degrees of freedom. The motion parameters output by SPM (rp*.txt) estimate head position relative to the first volume in 3D translation and 3D rotation, which are often entered as a nuisance regressor during individual-level statistics. Regressing the total displacement and relative position can potentially explain more variance in voxel-level BOLD signals that is related to head movement during an fMRI experiment.

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• SciCrunch
• 14 years ago - by Anonymous

Source code in Python for implementation of the warped linear mixed model. It automatically learns an optimal "warping function" (or transformation) for the phenotype as it models the data.

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• RRID-Legacy
• 10 years ago - by Anonymous

Leading global organization for investigation and collection of highly valuable and perishable geotechnical insights and data and timely distillation and provision of that information to public through reports.

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• RRID
• 3 years ago - submitted by Edyta Vieth

Model organism database that serves as central repository and web-based resource for zebrafish genetic, genomic, phenotypic and developmental data. Data represented are derived from three primary sources: curation of zebrafish publications, individual research laboratories and collaborations with bioinformatics organizations. Data formats include text, images and graphical representations.Serves as primary community database resource for laboratory use of zebrafish. Developed and supports integrated zebrafish genetic, genomic, developmental and physiological information and link this information extensively to corresponding data in other model organism and human databases.

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• SciCrunch
• 16 years ago - by Anonymous

Toolkit of MATLAB functions for computing integrated information ('phi' or 'Φ') from neural data. The toolbox consists of downloadable codes that perform practical computation.

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• RRID-Legacy
• 10 years ago - by Anonymous

Software Heritage provides service for archiving and referencing historical and contemporary software with focus on human readable source code. The site was unveiled in 2016 by Inria and is supported by UNESCO. The project itself is structured as non‑profit multi‑stakeholder initiative.

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• RRID
• 3 years ago - submitted by Anita Bandrowski

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14, 2026. Software tools which can perform Stochastic Tractography and related analysis on DWMRI data. Stochastic Tractography applies a Bayesian approach towards the estimation of nerve fiber tracts from DWMRI images.

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• SciCrunch
• 14 years ago - by Anonymous

Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis.

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• SciCrunch
• 10 years ago - submitted by Isabella Froman

Core provides services for maintaining Specific Pathogen Free status in macaque breeding colonies. Services include antibody detection in serum or plasma by Luminex-based assays and /or ELISA for SPF-agents like SIV, SRV, STLV, B virus, SFV. CMV, RRV, SVV, SV40, and LCV, and non-SPF infectious agents like measles, Burkholderia pseudomallei, Tripanosoma cruzi, Mycobacterium tuberculosis, and SARS-CoV-2. Offers services of cytokines quantification, and molecular assays for detection of SRV, CMV, SFV, and RRV.Performs nucleic acid purification from blood and tissue samples as well as qPRC for SIV viral load in plasma, cells, or tissue.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Provides comprehensive publication services for Univeristy of California affiliated departments, research units, publishing programs, and individual scholars who seek to publish original, open access journals, books, conference proceedings, and other scholarship. Content is delivered via research platform and is available to scholars worldwide.

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• SciCrunch
• 14 years ago - by Anonymous

Software toolkit for small-angle scattering data analysis from biological macromolecules.

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• RRID-Legacy
• 9 years ago - by Anonymous

Network of world class researchers and innovators to improve lives of people living in poverty by generating insights and tools for decision makers backed by rigorous, inclusive, and transparent research. Hub for research, training and innovation headquartered at University of California, Berkeley.

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• RRID
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE, documented on 7/28/13. Core facility of Columbia Neuroscience with the goal of establishing a collaborative and multi-investigator neuroimaging environment that is focused on the investigation of the neurocircuitry of the brain that underlies cognition, perception and action, and also the development of clinical applications that enhance the goals of personalized medicine. Within this environment the specific current research interests of the Hirsch group include several related directions of investigation. The first is conscious and subconscious neural processes that mediate emotion and cognition in healthy individuals and in patients with psychiatric disorders. This direction also includes neurocircuitry that is characteristic of disorders of consciousness such as minimally conscious or vegetative states, self and visual awareness, and attention. Neurocircuitry of other complex cognitive processes such as decisions, inductive and deductive reasoning, language, truthfulness and top-down influences of expectation, reward, and regulation on early visual and mid-level perceptual and emotional systems. On-going projects targeted for clinical applications include benefits for neurosurgery such as the development of task batteries to map the cortical locations of essential functions such as language, motor, sensation, memory, emotion and sensory functions including visions, audition and the chemical senses. Computational innovations for labeling correspondence between brain structure and specific functional regions are under development to achieve the highest interpretive precision. Current projects include integration of EEG and fMRI techniques to localize seizuregenic cortex in relation to eloquent and functioning cortex for neurosurgical planning; integration of TMS and fMRI to discriminate essential and associative language-sensitive cortical areas; and integration of VEP, EEG and fMRI to inform assessments of visual disease secondary to stroke or neural degeneration. Projects intended to refine and enhance diagnosis of psychiatric disorders such as anxiety, depression, and eating disorders include development of specialized paradigms to target dysfunctional neurocircuitry such as emotional systems (amygdala and basal ganglia) and control and regulatory systems (cingulate and pre-frontal cortex). Comparison of before-treatment images with after-treatment images to inform models of both treatment and disease and investigation of the hypothesis that individual genetic and functional differences have predictive value for treatment options and outcome are currently underway. The lab has pioneered techniques for functional mapping of single patients, and operates an active clinical service for mapping individuals for neurosurgical planning, assessments of the neurocircuitry that underlie acquired or inherited disabilities and the mechanisms of neuroplasticity that restore lost functions are actively investigated using both groups and single subject studies. :

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• SciCrunch
• 17 years ago - by Anonymous

Software for detection and reporting of spindle or slow oscillation events, simple automatic EMG artifacts, and their co-occurance or respective matching non-events. SpiSOP was designed to process large data quanta at once and multiple datasets in parallel.

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• RRID-Legacy
• 9 years ago - by Anonymous