Workflows

Minimum Deformation Template (MDT) Atlasin... (1)

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This pipeline present the redesigned automated workflow for constructing the Minimum Distance Template (MDT) atlas for a given population, based on one specific image modality (e.g., sMRI). There will be two specific validation examples based on 100+ ICBM subjects: Quantitative: The ICBM data will be registered to the MDT, NRU and ICBM 462 atlases and mean displacement stats across all subjects will be reported for each voxel. The distributions of these mean displacement magnitud...

Created: 2011-04-06 | Last updated: 2011-07-14

Credits: Pipeline

Automated Cortical Surface Extraction Work... (1)

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This workflow takes raw un-skull-stripped volumes and generates a cortical surface model using FreeSurfer? and CCB tools. Problem addressed by this workflow There are many ways to generate cortical surface models based on MRI data. Here is one of them. Eventually, there will be a new Learning-based Cortical Surface Modeling Pipeline, as well.   Input is Raw MRI T1-weighted volume CCB/FreeSurfer Cortical Surface extractor that the SIG-Shape team developed and we validated ...

Created: 2011-04-06 | Last updated: 2011-07-14

Credits: Pipeline

Local Shape Analysis (LSA) Workflow (1)

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This workflow takes raw un-skull-stripped volumes in 2 groups/populations and an ROI index to generate a color-coded shape object using the per-vertex local p-values of some local shape-measure (e.g., displacement, atrophy, Jacobian, curvature, etc). It also outputs the p-values color-map superimposed on the mean shape. Problem addressed by this workflow   Identifying local group differences between 2 populations in one specific ROI. This workflow also generates mean-shape DX mo...

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: Pipeline

Automated Image Registration (1)

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This is a simple registration workflow. The structural MRI images are aligned to a standard brain image by using AIR registration tools. To build this workflow follow the steps mentioned on the following pages. URL: http://www.loni.ucla.edu/Software/AIR Try this Pipeline Workflow Now!

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: Pipeline

Sub-Volume Probabilistic Atlas Segmentaito... (1)

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This workflow takes a raw unskull-stripped volume and a brain mask of the volume to create a tissue segmented image.This workflow is based on a novel genetic algorithm based finite mixture model and a local 3D Markov random field segmentation algorithm based on iterative conditional modes algorithm. Problem addressed by this workflow   This workflow performs tissue segmentation on the brain volumes using genetic algorithm based finite mixture model (GAMIXTURE), local 3D Markov ...

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: Pipeline

Global Shape Analysis Workflow (1)

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This workflow takes raw un-skull-stripped volumes in multiple groups/populations, or a Study-Design, and generates a scene file containing the models of the ROIs where the groups are different. It also reports the global 56 regional p-values. Problem addressed by this workflow   Identifying the group differences between 2 populations in the global shapes of 56 cortical and sub-cortical ROIs. This workflow also generates DX models of all 56 ROIs which can be viewed as a scene in Sh...

Created: 2011-04-06 | Last updated: 2011-04-06

Credits: Pipeline

Microsatellite-based Ancestry and Parentag... (1)

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GENEPOP is genetics software package that does the following types of analyses: Hardy Weinberg Exact Tests Linkage Disequilibrium Population Differentiation Nm estimates Basic Information, Fis and gene diversities Fst & other correlations File Conversion Additional Miscellaneous Utilities     Problems addressed by this GENEPOP workflow This specific GENEPOP workflow computes the following: Testing : Hardy-W...

Created: 2011-04-05 | Last updated: 2011-07-14

Credits: Pipeline

Integrated Mapping and Assembly with Quali... (1)

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This workflow contains the first step of a genomics data analysis protocol designed and implemented by Federica Torri, Fabio Macciardi and Ivo Dinov to process large number of sequence data outputted by the Illumina sequencing pipeline. See Step II analysis (GATK/QC/Cleaning) here. This protocol is implemented using the LONI Pipeline environment and includes the following types of computational resources: Mapping and Assembly with Qualities (MAQ) Sequence Alignment and Mapping t...

Created: 2011-04-05 | Last updated: 2011-04-05

Credits: Pipeline

PLINK Association workflow (1)

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PLINK is an open-source genome association analysis (GWAS) suite of tools providing a range of basic, large-scale computationally-efficient analyses. PLINK may be used for analysis of genotype/phenotype data, but requires some outside data-preprocessing (e.g., study design and planning, generating genotype or CNV calls from raw data). Support for visualization, annotation and storage of results is provided via gPLINK and Haploview.   The PLINK Association workflow provides testi...

Created: 2011-04-05 | Last updated: 2011-07-14

Credits: Pipeline

GWASS Impute (1)

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Genome-wide Association Study Software (GWASS) package provides genomics tools facilitating the analysis of genome-wide association studies. These tools were used in the design and analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC)   IMPUTE2 is a GWASS program for phasing observed genotypes and imputing missing genotypes. It includes basic and advanced functions. URL: http://www.loni.ucla.edu/twiki/bin/view/CCB/Pipe...

Created: 2011-04-05 | Last updated: 2011-04-05

Credits: Pipeline

mrFAST Indexing and Mapping (1)

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This page contains a number of bioinformatics workflows based on the mrFAST sequence analysis package. This page describes Pipeline bioinformatics modules from the mrFAST suite.   mrFAST (micro-read Fast Alignment Search Tool) is mapper designed to map short reads to reference genome with a special emphasis on the discovery of structural variation and segmental duplications. mrFAST maps short reads with respect to user defined error threshold, including indels up to 6 bp. This manu...

Created: 2011-04-05 | Last updated: 2011-04-05

Credits: Pipeline

EMBOSS-Matcher Pipeline Workflow (1)

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This page contains a number of bioinformatics workflows based on the advanced EMBOSS informatics package. This page describes as Pipeline modules several bioinformatics tools from the EMBOSS suite and demonstrates the construction of a couple of integrated pipeline workflows (end-to-end bioinformatics solutions via the LONI Pipeline). Matcher finds the best local alignments between two sequences. It can be used to compare two sequences looking for local sequence similarities using a ri...

Created: 2011-04-05 | Last updated: 2011-07-14

Credits: Pipeline

Bioinformatics BLAST processing Workflow (1)

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This is a simple workflow demonstrating a sequence Basic Local Alignment Search Tool (BLAST). This workflow shows an example of a common bioinformatics pipeline workflow using tools from several different institutions. This workflow starts by formatting the NCIBI/NCBI Escherichia coli (E. coli) database, creating a database-index table, using a FASTA query instructions to create a filtering file, and finally running miBLAST, an efficient Basic Local Alignment Search Tool (BLAST) for batc...

Created: 2011-04-05 | Last updated: 2011-04-05

Credits: Pipeline

Parsed UniProt to PubMed (1)

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Uses the parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve information from PubMed.

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Morgan Taschuk

Use UniProt to retrieve InterPro data (1)

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Used parsed Uniprot results (see workflowUsed parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from InterPro.

Created: 2011-04-01

Credits: Morgan Taschuk

UniProt to Gene Ontology (1)

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Used parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from Gene Ontology and outputs it in text format.

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Morgan Taschuk

Print Protein Information to HTML (1)

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Takes in a lot of parameters in order to construct an HTML table to display the information.

Created: 2011-04-01

Credits: Morgan Taschuk

Odkrywanie reguł asocjacyjnych za pomocą... (1)

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Proces pokazuje wykorzystanie algorytmu FP-Growth do odkrywania reguÅ‚ asocjacyjnych. Należy zwrócić uwagÄ™ na to, że implementacja algorytmu FP-Growth akceptuje jedynie atrybuty binominalne, zatem zachodzi konieczność zamiany wszystkich atrybutów numerycznych i nominalnych na binominalne.

Created: 2011-03-30 | Last updated: 2011-03-30

Vaccine Targets Workflow (3)

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Comparison of the genome of Bacillus anthracis to closely related strains will allow the discovery of proteins which may be involved in pathogenicity. Based on the biochemical pathways where the protein interacts, vaccines can be designed for these unique proteins. By gaining insight into the biochemical pathways that the unique proteins are involved in, the proteins can also be assessed for potential quality as vaccines. The key components of the vaccine finding system are the following: T...

Created: 2011-03-30 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

Compile Protein FASTA from Target to Drug ... (1)

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Uses a tab-delimited file with protein target and drug information (created in Ondex) to compile a protein FASTA file including each target.

Created: 2011-03-30 | Last updated: 2011-03-30

Credits: Morgan Taschuk Andrewsmeaton