Tuesday, January 10, 2017
Thursday, December 15, 2016
state charts for gene network modeling
Methods section is gotten from http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009376
Wednesday, December 14, 2016
gene network model
https://courses.edx.org/courses/course-v1:IEEEx+SysBio1x+3T2016/courseware/579a1cdc89624cfeaa18dabdd0785fcf/75147fb49bec4286979ab95e3b28326a/?child=first
Read the article: State charts for gene network modeling
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009376
Read the article: State charts for gene network modeling
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009376
Tuesday, December 13, 2016
Monday, December 5, 2016
time lapsed image analysis for yeast RLS meausrements
http://imagej.net/Batch_Processing
http://imagej.net/Scripting
http://imagej.net/How_to_apply_a_common_operation_to_a_complete_directory
**************
http://imagej.net/Scripting
http://imagej.net/How_to_apply_a_common_operation_to_a_complete_directory
**************
Tuesday, November 29, 2016
lab meeting 11/29/2016
1)a-DE gene lists for RNAseq project
Q1: there are various time points between control and treatment. Should we use the consensus DEG list?
IN the BGI report go to /Differential.../DEGList/
(There is an R package NOISeq)
BGI already did the analysis, we need to do a better job @11,12
check NOISeq in the report page 16/23-17/23-...
do a good job on that parts for a manuscript:
11-Pathway Analysis of DEG: functional enrichment phyer, hypergeormetric_distribution
12- PPI Analysis of DEG
It seems "GeneID" in BGI report are from NCBI. Example GeneID: 57573 is a standard ID.
1)b-Pathway analysis plan for DE gene lists
TODO: There are different sources of human gene/protein networks. We should try several for comparisons
TODO: We should try different clustering method, such as hlcust, mcl, etc (refer to Qin's previous paper for clustering analysis).
2)a-time-lapsed image analysis for yeast replicative lifespan
softwares:ImageJ, MATLAB, R
https://www.mendeley.com/groups/ gene -pathways/ pathway analysis
gene set analysis is a basic thing, we also need to do that.
data visualization course would be good for animations of .gifs
Q1: there are various time points between control and treatment. Should we use the consensus DEG list?
IN the BGI report go to /Differential.../DEGList/
(There is an R package NOISeq)
BGI already did the analysis, we need to do a better job @11,12
check NOISeq in the report page 16/23-17/23-...
do a good job on that parts for a manuscript:
11-Pathway Analysis of DEG: functional enrichment phyer, hypergeormetric_distribution
12- PPI Analysis of DEG
It seems "GeneID" in BGI report are from NCBI. Example GeneID: 57573 is a standard ID.
1)b-Pathway analysis plan for DE gene lists
TODO: There are different sources of human gene/protein networks. We should try several for comparisons
TODO: We should try different clustering method, such as hlcust, mcl, etc (refer to Qin's previous paper for clustering analysis).
2)a-time-lapsed image analysis for yeast replicative lifespan
softwares:ImageJ, MATLAB, R
https://www.mendeley.com/groups/ gene -pathways/ pathway analysis
gene set analysis is a basic thing, we also need to do that.
data visualization course would be good for animations of .gifs
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