October 2019 Wed Oct 2 ************* HW: netwwork on 3rd floor still at 10Mbps to outside world ADE to DNA [ 5] 0.00-10.00 sec 1.68 GBytes 1.44 Gbits/sec 46340 sender [ 5] 0.00-10.04 sec 1.67 GBytes 1.43 Gbits/sec receiver GUA to DNA [ 5] 0.00-10.00 sec 100 MBytes 84.0 Mbits/sec 1161 sender [ 5] 0.00-10.04 sec 99.8 MBytes 83.4 Mbits/sec receiver Cerberous to DNA [ 4] 0.00-10.00 sec 105 MBytes 88.4 Mbits/sec 421 sender [ 4] 0.00-10.00 sec 105 MBytes 88.4 Mbits/sec receiver DONE: sent note to ALL (lee, hisham, ramu, pedro, andrew and leon) setup screen savers ssds on all machines setup SCOPUS searches SW: zyper update on all reboots required gua rebooted along w/ all others SCI: GDash: ready for submit to NAR, reviewed w/ writting center reivew manuscript w/ bishop add note thanking sclick and j. gentle Generalized Step Parameters for Chrom.Folding question of math and algorithmic stability Kinking: interp is still critical do you really have the right data. 21 positions watch movie still need that kinking of histones vs sequence graphic TODO: update calendars Admin: DONE Ran defended his oral prelim and we sent not to Collin DONE submitted Letter rec for Zilong to tamar DONE sent copy of Zilong's paper to Tamar too DONE: BPS abstracts submitted see /autotmb/home/tmbshare/Public/Talks-and-Presentations/2020/Mar-BPS-Meeting/ clean up an dleave only the submitted version we want outlinmes of the talks there TODO hotel reservation: a.s.a.p. TODO bishop still needs to register flights *************************************** Rans Meetings TODO: a list of "missing" sims has been generated needs to be computed see list from email on 9/20 subject sims failed in tmb library see xls in /autotmb/home/rsu007/Public/sim-failed plan for completing: Three readme files one goes to Yeast/POS one goes to Yeast/NFR one goes to 601/posm02 What is expectation, reality, proposed fix(not this time) plan to confirm data really has slope of 2 graphical w/ VMD dcd to kink to VMD-viz... remake the plots = independent verification point checks that really have it right Zli Meeting TODO: unit tests python -w/ eye towards a comparison of integatrioan methods -look at GERM and see how they do integration w/ quaternions Magic Snake plans... outlines NanoCar plans .. outlines 10/9/2019 ***************** HW; now at 1Gbps for 3rd floor to world SW: nothing Admin: MOnday PHys210 Lecture for 10/14 talk w/ ran. TODO: give access to moodle and wiley and google drive chapter 24: E/M waves. overview of HW 24 TODO calendars for each SCI: G-Dash rejected NAR ??? TODO Ran and ZIlong show me their scopus searches confirm the searches what you need next summary of findings... save files on tmbshare/refs follow up on "interesting ones" by looking at citations to them next week download papers and review notes in okular LATER: install/upgrade to RNA to 15.1... date in november have it serve as backup for eve3ryting GUA,ADE no longer really needed plan for backups, solved by RNA cominb backup w/ 15.1 10/16/19 **************** HW: still full HDs ?? about move to E.A. SW: tmb5 maven install busted it; was needed for ibiomes-lite new nanocar uses old ibiomes-lite does not need maven newest version ibiomes-lite does not work b/c compiling issue NOT clear what the issue w/ the github version ibiomes-lite is TODO: asked to setup VM w/ ubuntu to see if ibiomes-lite install works any better ADM: tmb5 works now... roll-back zypper-dup fixed things TODO: bishop and zilong plan to upgrade RNA to 15.1 (from 42.3??) idea is 20Tb "scratch" on GUA and ADE once done PROPER PLAN (gua is backup only of home and ADE only of ibiomes) -size of current stuff -plan for "old" and "new" trajectories... can we push things to google or just delete -RNA as "staging' system -ADE/GUA as backups of websites/users respectively TODO: ran integrate blaine' 1us trajectory into the LitReviews: Scopus ClassFromRan: SCI: CTHL: 227: 4pm Ramu's talk on managing citations nature ref to TMBlibrary /autotmb/home/tmbshare/refs/Andrio2019-bioexcel-Modesto.pdf check hits on TMBlib/Gdash TMBlib@ACS 83 views total 10/16 GDash: 7 users last week; 1min avg use 1France + 5US(tx,IL,LA-Tech) TMBlibrary: 7users; 2 germany + 5 US(KS + LA-Tech) review of manuscript from NAR 10/30/19 ************ HW: update RNA to 15.2 still needs to be done ??? SW: ibiomes-lite precompiled version works fine w/ Java 1.7 or 1.8 NOT a problem b/c can still change banner and other info PROBLEM is that precompiled versions are no longer available have to get them from tar balls that we have java 1.7 and 1.8 are being retired so evenn the precompiled won't work CHOICE: either use precompiled/old version or update ibiomes-lite to work w/ maven/java 1.11 or find/develop another tool compiling ibiomes-lite from teh github version does not work Maven and Ubuntu final answer for ibiomes-lite? https://www.infoq.com/articles/upgrading-java-8-to-12/ -ubuntu did not work any better than Op0ensuse -long term life of ibiomes-lite.. -ANOTHER solution ? tell me next week ibiomes-lite: QM and MD ibiomes-lite requires java-1.7 (7 and 8 are similar; after that all changed) current java is 1.11 short recipe to find the errors is from https://github.com/jcvthibault/ibiomes/blob/master/ibiomes-lite/README step 2 is broken in the following... MVN does not install the install reports the errors that it runs into NOTE for mvn install to work it must already be installed/configured on your machine Steps: 1. Get a copy of the ibiomes source code 2. Compile ibiomes project a. Go to ibiomes projet root folder (or ibiomes-lite/ folder if you only want to build this component) b. Run 'mvn install -DskipTests' 2. Set $IBIOMES_HOME to point to the root of the iBIOMES project folder 3. Add $IBIOMES_HOME/ibiomes-lite/scripts to your $PATH 4. Copy the folder ibiomes-lite/lite-web/ to your web directory (e.g. ~/public_html/) 5. Set $IBIOMES_LITE_WEBDIR to point the new lite-web folder ((e.g. ~/public_html/lite-web/) ADM: RSU: preproposal -finished into and will complete this week (draft by Thursday AM) -done w/ labs on thursday -two lab reports -grades assembled by Tuesday 11/5 w/in timeline for graduating seniors ZLI: thesis -leave him alone and let him write - SCI: lit. reviews WEB: CIMM: https://cimmhub.laepscor.org is working GDASH: 9last week; 7US and 1 india ; 1 belgium; 2:14min avg time TMB-LIBRARY: 7users; 3US + 2UK + 1france + 1 russia ; 1:26 avg time TMBLibr at ACS: 109 views and "published" verified that GDash-VM is on google drive at 13GB TODO: ran update the group web page publications to pont to this