Workflows

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Type: LONI Pipeline
Original Uploader

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

Created: 05/04/11 @ 22:05:03 | Last updated: 05/04/11 @ 22:05:11

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 95 times | Downloaded: 31 times

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Original Uploader

Workflow Automated Brain Tissue Extraction and Volu... (1)

Created: 06/04/11 @ 00:57:47 | Last updated: 14/07/11 @ 01:05:58

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes raw un-skull-stripped volumes and generates tables of the volumes for all 56 ROIs currently automatically extracted using LONI BrainParser.   Problem addressed by this workflow Computing and tabulating the Brain Volumes 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 ShapeViewer.   Detailed Workflow Usage & Specifications Input: Any volumetric file format can be use...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 24 times | Downloaded: 9 times

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Original Uploader

Workflow Deformable Organisms Skullstripping (1)

Created: 14/09/11 @ 23:13:44

Credits: User Azamanyan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Overview - Deformable Organisms Skullstripping Pipeline will skull-strip an magnetic resonance (MR) image of the brain using a deformable organisms framework. Problem addressed by this workflow Segment or delineate the brain in whole head MR images. Creates a mask of the brain, separating it from skull, skin, eyes, neck, and cerebro-spinal fluid (CSF). Detailed Workflow Usage & Specifications The module takes ANALYZE or NIFTI magnetic resonance images of the head as input a...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 9 times | Downloaded: 2 times

This Workflow has no tags!

Original Uploader

Workflow Bioinformatics BLAST processing Workflow (1)

Created: 05/04/11 @ 21:17:52 | Last updated: 05/04/11 @ 21:43:46

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 31 times | Downloaded: 12 times

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Original Uploader

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

Created: 06/04/11 @ 00:24:00 | Last updated: 06/04/11 @ 00:24:06

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 14 times | Downloaded: 6 times

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Original Uploader

Workflow Image Registration Meta Algorithm (IRMA) (1)

Created: 06/04/11 @ 01:39:08 | Last updated: 14/07/11 @ 01:09:06

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Overview - Workflow-Title In this workflow different registration algorithms are applied to the same image and the image that is best registered to the template is chosen as the output top candidate.   Problem addressed by this workflow In this workflow various registration algorithm is performed on the same subject. The algorithm that gives the best result is chosen. This might be different for different input images. This workflow is robust and picks the best-registered imag...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 17 times | Downloaded: 5 times

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Original Uploader

Workflow Fdist2 Simulation Pipeline Workflow (1)

Created: 08/03/12 @ 18:22:41 | Last updated: 08/03/12 @ 20:30:28

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Fdist2 is a simulation program to detect loci that might be under selection in samples from structured populations.   Workflow Usage & Specifications The workflow reads an input file "fdist_params2.dat", which consists of 6 lines. This file must only contain numbers in the format described: Total number of demes (100 max). No of populations sampled (must be less than or equal to total number of demes). Expected Fst for infinite allele, infinite island model. Sample si...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 10 times | Downloaded: 12 times

This Workflow has no tags!

Original Uploader

Workflow GWASS Impute (1)

Created: 05/04/11 @ 21:53:02 | Last updated: 05/04/11 @ 21:53:52

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 36 times | Downloaded: 8 times

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Original Uploader

Workflow Automated Cortical Surface Extraction Work... (1)

Created: 06/04/11 @ 00:44:05 | Last updated: 14/07/11 @ 00:20:57

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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 ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 23 times | Downloaded: 6 times

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Original Uploader

Workflow Mouse Brain Image Analysis: General Linear... (1)

Created: 06/04/11 @ 01:52:56 | Last updated: 06/04/11 @ 01:53:01

Credits: User Pipeline

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Overview - General Linear Model The workflow runs voxelwise statistics on two populations of mice. Each of the populations has been scanned prior to injection of a label and at four subsequent timepoints.   Problem addressed by this workflow The workflow addresses several problems. First of all, it performs co-registration between the subjects from the two populations and at different timepoints. It then scales all images. Finally, it runs a multiple linear regression module t...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 41 times | Downloaded: 8 times

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