Iibis - Recent changes [en]

Plink Pipeline on Quarry

2009-11-20T22:32:57Z

Run GenPBSscript.m on Quarry:

LAB-091124

2009-11-19T21:34:33Z

Tasks:

New page

{{ShenLabHeader}}

=Agenda=

== Tasks ==
* Focuses
** Sungeun: Imaging Genetics, CTSI Classification, IGB (Python), Parameterization
** Kwangsik: GWAS, Imputation, FreeSurfer/SurfStat, Classification
** Jing: Genetics of Hippocampal morphometry, FASD facial analysis, Parameterization, SPHARM+FreeSurfer+SurfStat
** Shanker: CNV/GenomeStudio, Imaging Genetics
* Discussion
** Collect some existing data for validation
** Journal club: machine learning, surface modeling, GWAS?
** Mouse CIFASD, bone analysis
*** Features: landmarks, measures, geometry, density (future)
**** How to model the geometry (alignment)? Size, asymmetry, curvature
*** Outcomes: diagnosis (Alcohol vs. control), FAS vs FASD
*** Covariates: head size, total bone volume, landmark size
*** Methods: SVM, RVM, individual + joint analyses
*** Current issues: matlab variable, scalability, superimpose on volume
** Supercomputers: (1) Imputation, (2) Matlab compilation
** Multiple testing and power analysis
** CNV data analysis
** Region-based IGB, APC, QC'ed phenotype, CTSI-imputation, replication, parallelism
** Wiki backup: http://pypi.python.org/pypi/mwlib.rl/0.9.11
** Segmentation and Registration: Amira; ITK-SNAP; Slicer; FreeSurfer: http://surfer.nmr.mgh.harvard.edu/; STAPLES + ANTS; FreeSurfer + LDDMM; Levelset segmentation: bdong@math.ucla.edu, http://www.math.ucla.edu/~xbresson/code.html.
** Interpretation: Pathway analysis; Graph/Network toolboxes, http://erzuli.ss.uci.edu/R.stuff/, http://www.indiana.edu/~cortex/connectivity.html, http://nwb.slis.indiana.edu/, http://www.graphviz.org/
** Clustering on various measures: p-values, regression coefficients, etc.
** Imaging Genetics Databases (CS/Informatics)
** SPHARM-MAT Release: December?
*** SPHINX doc, website/MySQL, wiki to PDF, SPHARM-MAT GUI and Visualization in Python
*** SPHARM documentation: http://195.251.6.234/armada/

== Papers ==

* Image and Vision Computing
** MICCAI 2010: http://www.kent.ac.uk/miccai/future_conferences.php, Beijing, 9/20-24
** MIAR: http://www.miar.org/2010/, '''4/23/10''', Beijing, 9/19-20
** ECCV: http://www.ics.forth.gr/eccv2010/, '''3/10/10''', Hersonissos, Crete, Greece, 9/5-11
** ICIP: http://www.icip2010.org/, '''1/11/10''', Hong Kong, 9/12-15
* Shape Modeling and Analysis
** SMI: http://www.smi2010.lsis.org/symposia/browse/SMI10, '''12/4/09''', Arts et Métiers ParisTech, Aix-en-Provence, France, 6/21-23
** 3DPVT: http://www.3dpvt2010.org/, '''12/16/09''', Paris, France, 5/17-20
* Neuroimage
** ICAD: http://www.alz.org/icad/, '''2/1/10''', Honolulu, Hawaii, 7/10-15
** OHBM: Barcelona, Spain, 6/6-10
* Topics
** Genetics of hippocampal morphometry (MCI): MICCAI/MIAR (Jing)
** EM methods for MCI-AD classification using imaging and genetics: MICCAI/MIAR (Sungeun)
** Imaging genetics of BL cortical data (ADNI): ICAD/OHBM/Journal (Kwangsik)
** Classification using ADNI phenotypes: Journal (Kwangsik)
** Imaging genetics of BL FS/VBM (ADNI): ICAD/OHBM/Neuroimage (Li)
** Imaging genetics of FDG/PIB and other markers (ADNI): ICAD/OHBM/Journal (Sungeun)
** Genetics of CSF biomarkers (ADNI): ICAD/OHBM/Journal (Shanker)
** Human CIFASD, facial imaging analysis: ?/Journal (Jing)
** Mouse CIFASD, bone analysis: ICIP/Journal (?)
** SPHARM-MAT: OHBM (Sungeun)

== Schedule ==
* 11/24, Shanker, TBD
* 12/01, Kwangsik, TBD
* 12/08, Li, discussion
* 12/15, Jing, TBD
* 1/5, Sungeun, TBD

IGL Meeting Notes

2009-11-19T21:30:34Z

ShanLab:

←Older revision		Revision as of 21:30, 19 November 2009
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		+	\| [[LAB-091124]]
	\| [[LAB-091110]]		\| [[LAB-091110]]
	\| [[LAB-091103]]		\| [[LAB-091103]]

Wiki maintenance notes

2009-11-18T16:22:37Z

←Older revision		Revision as of 16:22, 18 November 2009
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	* The link in the below is about a python app to create PDFs from meidawiki articles.		* The link in the below is about a python app to create PDFs from meidawiki articles.
	** http://pypi.python.org/pypi/mwlib.rl/0.12.3		** http://pypi.python.org/pypi/mwlib.rl/0.12.3
		+
		+	* Radiology wiki contact: Kohli, Marc David, mkohli@iupui.edu

Planning

2009-11-18T15:57:43Z

New page

{{CfNPlanningHeader}}

* http://nihroadmap.nih.gov/: To be considered transformative, projects must have the potential to create or overturn fundamental scientific paradigms through the use of new and novel approaches or to lead to major improvements in health through the development of highly innovative therapies, diagnostic tools, or preventive strategies.
** Gene-Behavior => Gene-System-Behavior => Gene-Cell-System-Behavior => systems biology/pathway.

Shenlab

2009-11-18T15:50:49Z

Others:

←Older revision		Revision as of 15:50, 18 November 2009
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	** [[Segmentation with STAPLES]]		** [[Segmentation with STAPLES]]
	* [[IGL_Projects]]		* [[IGL_Projects]]
		+	* [[Planning]]

	=Pipelines=		=Pipelines=

←Older revision		Revision as of 22:32, 20 November 2009
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	*** (PBSscript sample: /N/soft/linux-rhel4-x86_64/plink-1.06/bin/plink --bfile /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/genotype/ADNI_SNP_09_PSUB --pheno /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/phenotype/Adj_APC_MNI.txt --all-pheno --assoc --missing-phenotype -99999 --adjust --qt-means --extract All_1640files_94336to20406snps.txt --out /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/Out/ADNI_SNP_09_PSUB_Adj_APC_MNI_assoc_snps)		*** (PBSscript sample: /N/soft/linux-rhel4-x86_64/plink-1.06/bin/plink --bfile /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/genotype/ADNI_SNP_09_PSUB --pheno /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/phenotype/Adj_APC_MNI.txt --all-pheno --assoc --missing-phenotype -99999 --adjust --qt-means --extract All_1640files_94336to20406snps.txt --out /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/Out/ADNI_SNP_09_PSUB_Adj_APC_MNI_assoc_snps)

-	** Case 4: assoc_mperm (--mperm ~~5000~~ --extract mysnps.txt)	+	** Case 4: assoc_mperm (--mperm 10000 --extract mysnps.txt)
	*** Select Binary Input: select the genotype file, e.g., ADNI_SNP_09_PSUB.bed		*** Select Binary Input: select the genotype file, e.g., ADNI_SNP_09_PSUB.bed
	*** Select Covariates: (1) select one, or (2) click cancel		*** Select Covariates: (1) select one, or (2) click cancel
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	*** Enter an association method: --assoc		*** Enter an association method: --assoc
	*** Enter an output prefix: '''assoc_mperm'''		*** Enter an output prefix: '''assoc_mperm'''
-	*** Enter other options: --missing-phenotype -99999 '''--mperm ~~5000~~ --extract /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic_01/genotype/All_files1865_snps114115t32723u.txt'''	+	*** Enter other options: --missing-phenotype -99999 '''--mperm 10000 --extract /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic_01/genotype/All_files1865_snps114115t32723u.txt'''
	*** (PBSscript sample: /N/soft/linux-rhel4-x86_64/plink-1.06/bin/plink --bfile /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/genotype/ADNI_SNP_09_PSUB --pheno /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/phenotype/Adj_APC_MNI.txt --all-pheno --assoc --missing-phenotype -99999 --adjust --qt-means --extract All_1640files_94336to20406snps.txt --out /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/Out/ADNI_SNP_09_PSUB_Adj_APC_MNI_assoc_snps)		*** (PBSscript sample: /N/soft/linux-rhel4-x86_64/plink-1.06/bin/plink --bfile /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/genotype/ADNI_SNP_09_PSUB --pheno /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/phenotype/Adj_APC_MNI.txt --all-pheno --assoc --missing-phenotype -99999 --adjust --qt-means --extract All_1640files_94336to20406snps.txt --out /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/Out/ADNI_SNP_09_PSUB_Adj_APC_MNI_assoc_snps)

-	** Case 5: assoc_mpall (--mperm ~~5000~~)	+	** Case 5: assoc_mpall (--mperm 10000)
	*** Select Binary Input: select the genotype file, e.g., ADNI_SNP_09_PSUB.bed		*** Select Binary Input: select the genotype file, e.g., ADNI_SNP_09_PSUB.bed
	*** Select Covariates: (1) select one, or (2) click cancel		*** Select Covariates: (1) select one, or (2) click cancel
Line 62:		Line 62:
	*** Enter an association method: --assoc		*** Enter an association method: --assoc
	*** Enter an output prefix: '''assoc_mpall'''		*** Enter an output prefix: '''assoc_mpall'''
-	*** Enter other options: --missing-phenotype -99999 '''--mperm ~~5000~~'''	+	*** Enter other options: --missing-phenotype -99999 '''--mperm 10000'''
	*** (PBSscript sample: /N/soft/linux-rhel4-x86_64/plink-1.06/bin/plink --bfile /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/genotype/ADNI_SNP_09_PSUB --pheno /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/phenotype/Adj_APC_MNI.txt --all-pheno --assoc --missing-phenotype -99999 --adjust --qt-means --extract All_1640files_94336to20406snps.txt --out /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/Out/ADNI_SNP_09_PSUB_Adj_APC_MNI_assoc_snps)		*** (PBSscript sample: /N/soft/linux-rhel4-x86_64/plink-1.06/bin/plink --bfile /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/genotype/ADNI_SNP_09_PSUB --pheno /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/phenotype/Adj_APC_MNI.txt --all-pheno --assoc --missing-phenotype -99999 --adjust --qt-means --extract All_1640files_94336to20406snps.txt --out /N/dc/projects/shenlab/subjects/GWAS/GWAS-ADNI-shenli/Data/genomic/Out/ADNI_SNP_09_PSUB_Adj_APC_MNI_assoc_snps)