Curator Dashboard

Data collection of gene expression patterns mapped in whole-mount mouse embryo (ICR strain) of mid-gestational stages (Embryonic Day 9.5, 10.5, 11.5), in which most striking dynamics in pattern formation and organogenesis is observed. Collection of gene expression patterns of transcription factors (TFs) and TF-related factors such as transcription cofactors. Genes were extracted from databases including RIKEN Transcription Factor Database and Panther Classification System.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

A database and storage service resource which allows users to create, view, share, and download information from companion websites. RunMyCode allows users to create companion websites for their scientific publications. Users can share and download computer code and data from companion websites made with RunMyCode. Any software and data format is compatible with RunMyCode.

• Resource
• SciCrunch
• 12 years ago - submitted by Kristen Jensen

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Implementation of a database of ionic conductance models stored in simulator-independent NeuroML format, with a parser to convert the representation into GENESIS simulation scripts. It was developed as a means of sharing channel models between different neural simulators. It is also one of the first core components of the Modelers Workspace (MWS). At present, ChannelDB is implemented as a stand-alone module, with its own graphical user interface to the database, which is implemented with MySQL. After further development, the ChannelDB GUI will be merged into the MWS. The NeuroML development kit parser (from http://www.neuroml.org/ndk.html) is used to create Java objects from the NeuroML format XML files stored in the database. These are then accessed with Java software to create simulation scripts for the particular simulator. The first implementation of a parser to create simulation scripts is for GENESIS. The files in this package will let you * Search a small remote database of ion channel models to retrieve and view their descriptions and NeuroML representations, and generate simulator scripts from the model representation. * Set up your own database of ion channel models * Extend ChannelDB with the addition of parsers for other simulators, and with Java classes to cover other types of channels.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Software homology search tool for huge short reads generated by next-generation sequencers.Can detect remote homologs like BLAST and is about 40 times more efficient than BLAST by using a GPU-computing technique.

• Resource
• SciCrunch
• 12 years ago - by Anonymous

Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

An organization that is centered around the education of younger Parkinson's disease patients as well as their families, friends and healthcare professionals. They primarily provide educational and support programs and services that are designed to help younger Parkinson's patients manage the disease and maintain a healthy lifestyle. The center provides information about treatment options, clinical trials, support groups, person to person chats, local chapters,regional referral information, and Parkinson's related events.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

A python toolbox for analysis of MRI images. It relies on calls to a number of widely tested algorithms from the FMRIB software library (FSL) and the advanced normalization tools (ANTS) to provide analysis of simultaneously acquired ASL/BOLD fMRI data. It was developed for analyzing the datasets collected as part of the Cincinnati MR Imaging of NeuroDevelopment (C-MIND) project.

• Resource
• SciCrunch
• 11 years ago - submitted by Kristen Jensen

A reference-guided assembler comprising of two main modular programs: MosaikBuild and MosaikAligner. MosaikBuild converts various sequence formats into Mosaik?s native read format. MosaikAligner pairwise aligns each read to a specified series of reference sequences and produces BAMs as outputs. At this time, the workflow consists of supplying sequences in FASTA, FASTQ, Illumina Bustard & Gerald, or SRF file formats and producing results in the BAM format. Unlike many current read aligners, MOSAIK produces gapped alignments using the Smith-Waterman algorithm. MOSAIK is written in highly portable C++ and currently targetted for the following platforms: Microsoft Windows, Apple Mac OS X, FreeBSD, and Linux operating systems. Other platforms can easily be supported upon request. MOSAIK is multithreaded. If you have a machine with 8 processors, you can use all 8 processors to align reads faster while using the same memory footprint as when using one processor. MOSAIK supports multiple sequencing technologies. In addition to legacy technologies such as Sanger capillary sequencing, our program supports next generation technologies such as Roche 454, Illumina, AB SOLiD, and experimental support for the Helicos Heliscope.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Software package for reconstructing three-dimensional models of brain structures from 2-D delineations using a customizable and reproducible workflow. 3dBAR also works as an on-line service (http://service.3dbar.org) offering a variety of functions for the hosted datasets: * downloading reconstructions of desired brain structures in predefined quality levels in various supported formats as well as created using customizable settings, * previewing models as bitmap thumbnails and (for webGL enabled browsers) interactive manipulation (zooming, rotating, etc.) of the structures, * downloading slides from available datasets as SVG drawings. 3dBAR service can also be used by other websites or applications to enhance their functionality. * Operating System: Linux * Programming Language: Python * Supported Data Format: NIfTI-1, Other Format, VRML

• Resource
• SciCrunch
• 15 years ago - by Anonymous

An MRI resource which provides age-appropriate images of children. It includes an average, age-appropriate T1-weighted image, constructed from 130 typically developing children ages 6-to-10 and a set of 32 resting-state ICA components. These components were generated from 494 typically developing children, ages 6-to-10 years old, using the MELODIC ICA tool, bootstrapped with 1000 resamples. Both of these resources are described in detail in a manuscript submitted for publication.

• Resource
• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Web tool as secondary structure prediction method, incorporating two feed forward neural networks which perform analysis on output obtained from PSI-BLAST. Web server offering analyses of protein sequences.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

An infrastructure for managing of diverse computational biology resources - data, software tools and web-services. The iTools design, implementation and meta-data content reflect the broad NCBC needs and expertise (www.NCBCs.org).

• Resource
• SciCrunch
• 14 years ago - by Anonymous

ITK-based processing and 3D Slicer scene management in ParaView. It is meant to broaden the use of ParaView for high performance computing and visualization in the medical imaging research community. The effort is focused on developing ParaView plug-ins for managing VTK structures from 3D Slicer MRML scenes and encapsulating ITK filters for deployment in ParaView.

• Resource
• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software that is designed to take Illumina sequence data, a MLST database and/or a database of gene sequences (e.g. resistance genes, virulence genes, etc) and report the presence of STs and/or reference genes.

• Resource
• SciCrunch
• 9 years ago - submitted by Michael Li

The Australian Microscopy & Microanalysis Research Facility (AMMRF) is Australia''s leading facility for the characterisation of matter on a fine scale. We specialise in instrumentation, methodologies and applications for characterising samples in the physical, biological and environmental sciences using ion and electron beams, scanned probes, X-rays as well as light and laser optics. The six AMMRF nodes are located at the host universities in Adelaide, Brisbane, Canberra, Perth and Sydney. More information is available at www.ammrf.org.au and at http://www.ammrf.org.au/techniquefinder.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

A Matlab-based toolbox initially created for reading, writing, and processing of BrainVoyager (QX) files in Matlab.

• Resource
• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Curated database of known (published) gene lesions responsible for human inherited disease.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

GpetView is light-weight image viewer based on Gtk+ library. The supported image format is ANALYZE(TM) format (Mayo Foundation ). GpetView can run on Unix-systems, such as Linux, Solaris, IRIX, Mac OS-X etc. From Version 2.0, GpetView can also run on Win32 system, if you have installed Glib and Gtk+(2.x). Glib andGtk+ can be found at http://www.gtk.org. For Windows users, you can find Gtk+ libraries at http://gladewin32.sourceforge.net/modules/news/ GpetView has the following features: * very light-weight * view images as transverse, coronal, or sagittal * change color-map (support Analyze lkup file) * zoom images * ROI (Region-Of-Interest) with shapes of circle, ellipse, rectangle, polygon and automatic edge detection * Image histogram and profile Sponsors: This resource is supported by Osaka University. Keywords: Image, Viewer, Software, Transverse, Coronal, Sagittal, Map, Histogram,

• Resource
• SciCrunch
• 17 years ago - by Anonymous

An implementation of standard PCA algorithms for use on scalar or vector data sets. Kernel PCA is implemented in this class, where the data sets are scalar or vector valued functions assigned at each of the points in a PointSet. A Gaussian Distance Kernel class is provided with the PCA class.

• Resource
• SciCrunch
• 11 years ago - submitted by Kristen Jensen