March 2019
***************
HW: 
	CIMMHUB: still running?
	chk w/ karthik next week about certificate
	
	CYT: automat the certificate

SW:
	Matlab licenses setup
	will 

NOTES: I'm not doing either LBRN or CIMM meeting

PLAN:  
	Spring 1/4:
	I teach MWF 12:30-1:30
	Lab Wed 2-6
	LesHouches... what's my talk.... 
		find an xyz model from HiC of yeast
		we know we can do an entire chromosome
			2-angle model from Schlicks' models
			2-angle model from yeast
	papers?
	MONDAY is SGCI meeting?

KITP; everaers and dekker summer 2020 
	https://www.kitp.ucsb.edu/activities/chromosomes20
gordon conf. even years 2020 is next
https://www.grc.org/chromatin-structure-and-function-conference/2020/

epigenetics: https://www.grc.org/epigenetics-conference/2019/

2019 ISCB
https://www.iscb.org/cms_addon/conferences/ismbeccb2019/schedule/schedule.php


TODO:
	get https://www.sciencedirect.com/science/article/pii/S1046202316304662
	see /autotmb/home/tmbshare/refs/Dekker2017.pdf

	review the issue on 4D nucleome
		https://www.sciencedirect.com/journal/methods/vol/123/suppl/C

ZLI
FIND THE HIGHEST RESOLUTION Yeast Hi-C model available
	xyz file
RSU:
MD sims of nucleosome
DNA kinking from BPS and other



Wednesday march 13
***********************
HW: CIMMHub... zli responsible for monitoring it
	zli responsible for g-dash/nanocar monitoring
	rsu responsible for ibiomes report

SW: zypper update
	matlab 2019a zli ??? when';s it coming and updating licenses

MEETINGS:
	CIMM is  friday no-one is going
	LBRN april 5/6 bring same posters, same abstracts...
		zli and rsu will go
	Albany meeting
	SGCI bootcamp ??   ran follow up w/ my email

RSU: md sims/nucleosome?
	winnograph is last publication on MD sims
	coarse-grained sims at BPS at UMD, Hao Wu in JChemPHysics
RSU: DNA kinking

ZLI:  hi-C models yeast. what format?
	 see https://www.biorxiv.org/content/10.1101/103614v5  DNASeI and 3D conf correlate   
	https://www.ncbi.nlm.nih.gov/pubmed/27723753  Micro-C... 23 citations! which one has xyz?
	OR how TO CONVERT TO XYZ

ZLI follow up
DECIPHERING HI-C DATA INTO POLYMER DYNAMICS
Soya Shinkai1,2; Masaki Nakagawa2,3; Takeshi Sugawara2,4; Yuichi Togashi2,5; Hiroshi Ochiai5; Ryuichiro Nakato6; Yuichi Taniguchi7; Shuichi Onami1; 

ZLI and RSU see abstracts in 
/autotmb/home/tmbshare/Public/Conferences/2019/LesHouches


	
PAPERS:
SCIENCE: rsu and on-demand sims...
	
DEFINE WHO IS DOING WHAT AND WHAT'S TIMELINE

b/4 LesHOuches
	Ran will have preerpint 601 kinks posted
	zli will have xyz for Hi-C into G-Dash
		nanocar for education submitted
Spring:
	ZLI: MS oral/ PHd oral
		G-dash redo		
		magic snake
	RSU:  phd oral
		NuBuilder
		HP normal modes -> published
	
Summer:
	RSU: NuBUilder for ANY pdb DBP in RCSB
		publish NuBuilder -> publish
	ZLI:  	G-dash kernel in python summer publication
		tricks for optimization
		fitting of Hi-C data
			(Elizabeth Villa MMFF fro VMD/NAMD and Kschulten)

NOTES from SGCI meeting
		required software
		NAMD (py) simple install untar
		VMD (py) robust installer...esp. w/out graphics
		Ambertools (py)   required compile
		3DNA (no py)  untar/unzip
		Lammps (py)  untar?
		ICMtools (fortran: compilers..) -> HPTools in python
			
		PythonModules
			2bitreader
			pybigwig (missing some dependencies on CYT)
			wig2bigwig
			pipinstall 2.7 
			
			numpy 
			
		Java Script:  JSmol/BIodalliance -> local copies
			java version maybe an issue
			



March 27
**************
SW: NA
HW: NA
Science:
TmB-ibiomes
	copyright done... out for review'
	just waiting
LBRN posters
	same as BPS meeting
	please try to engage w/ Hudson ALpha, NYU and other speakers
LesHouches Talk
	tom's will do this afternoon
SPARK:  done... think systematically
	works for making figures from concept
	or for making figure from text
		both cases helps to solidify idea
G-Dash:
SGCI: 
bioinformatics class