January 2016 Group Meeting 1/08/2016 ********************** 3:30: anthony and dilip ran and anik excused TODO: bishop double check to make sure denis is on emails HW: tmb3 still dead /home/ still way full/overfull 4.8 TB left 94% full trajectory decision for achiving SW: anthony will do updates on all Hub: 138.47.29.74 enter in local /etc/hosts of DNA as tmbhub.coes.latech.edu running w/ debian (wheezy 7.9) and hubzero2.0 TODOs: document HOWTO: /home/tmbshare/docman/Hub-HowTo install and config of the OS install and config of the hub make the above at very simple formatted html READmE like documents development plan? ?rwhat triggeers a reinstall and how much time for that ?hardware? dvd vs cd vs old opeteron boxes SOS: bishop will be doing a SOS talk in S'port and need the Little Fe 1/15/2016 ********************** HW: rna still out of space backups need to be checked on gua and ade tmb3 getting restored (???) by anthony maybe SW: tmb1 115% vlc 16-yeast-positions.mpg VLC media player 2.2.1 Terry Pratchett (Weatherwax) (revision 2.2.1-0-ga425c42) [0000000001a73eb8] core demux error: corrupt module: /usr/lib64/vlc/plugins/access/libdvdnav_plugin.so [00000000019a00b8] core libvlc: Running vlc with the default interface. Use 'cvlc' to use vlc without interface. [00007f8600000e88] core demux error: corrupt module: /usr/lib64/vlc/plugins/access/libdvdnav_plugin.so setNativeLocks failed: Resource temporarily unavailable [00007f8600c03cd8] avcodec decoder: Using NVIDIA VDPAU Driver Shared Library 340.96 Sun Nov 8 22:09:55 PST 2015 for hardware decoding. [00007f8600c15ab8] core demux error: corrupt module: /usr/lib64/vlc/plugins/access/libdvdnav_plugin.so setNativeLocks failed: Resource temporarily unavailable [00007f8600c03f48] avcodec decoder: Using NVIDIA VDPAU Driver Shared Library 340.96 Sun Nov 8 22:09:55 PST 2015 for hardware decoding. [00007f8600c02dd8] core demux error: corrupt module: /usr/lib64/vlc/plugins/access/libdvdnav_plugin.so but the image still looks good! JabRef works and now so does jabref Science ********* Hub: /home/tmbshare/docman/HubHowTo/ is still empty.. anthony has volunteered to do this. still no notes form dilip on hub install status report from dilip apparently no "history" dump exits for install command but rather handnotes check w/ dilip RAN: dsdna ; has issues send "instruction set" to group and put it in the svn repo pyton modules being updated s.t. run anywhere look at the ibiomes PAPERS see tom cheatham's website and or pubmed or the google ibiomes provides the refs Anik: models w/ nucA 1/22/16 ************ RAN: organize a short lit. review of nucleosome dynamics JBSD paper reviewed by bishop NAR paper under review by bishop earlier review for BJ by bishop review the manuscript by Suma and Bishop that's in works still Anik: reports on running dsdna using ran's instructions bishop confirms make and review nucA models AAA: post open suse install notes look for a site on bishop's web http://dna.engr.latech.edu/~aaa029/Guide%20for%20PXE%20Boot%20by%20Anthony%20Agee.html forward this littlefe folks listserve DISCUSSION: necessary and sufficient set of analysis for nucleosomes how to make namd run an arbitrary TCL/shell script in background 1/29/16 ********* discuss a benchmarks for bluewaters 3DNA, vmd, hub: progress on hiub configuration openldap rappture pegasus submit configuration of hub menus fqdn from danny configured update the howto/docman in tmbshare