January 2014 - Release-team - mailman3.cels.anl.gov

modules that (might) depend on workspace_service
by N.L. Harris 07 Jan '14

07 Jan '14

bash-3.2$ grep -r -i workspace_service */DEP* KBaseFBAModeling/DEPENDENCIES:workspace_service analysis_book/DEPENDENCIES:workspace_service experiment/DEPENDENCIES:workspace_service gwas/DEPENDENCIES:workspace_service meme/DEPENDENCIES:workspace_service prom_service/DEPENDENCIES:workspace_service ribo16s_pipeline/DEPENDENCIES:workspace_service bash-3.2$ analysis_book is obsolete experiment is no longer in use

1 0

Re: [Release-team] [Kbase-devel] Janurary release - time to start gathering info
by Mundy, Michael B. (Mike) 06 Jan '14

06 Jan '14

I merged the wsdeluxe branch to master for the probabilistic annotation service and it is ready for deployment. Mike Mundy | Senior Analyst Programmer | Bioinformatics Systems Unit | 507-266-7232 | mundy.michael(a)mayo.edu Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org <http://www.mayoclinic.org> On 1/3/14 10:18 AM, "Mundy, Michael B. (Mike)" <Mundy.Michael(a)mayo.edu> wrote: >Miriam, > >The probabilistic annotation module is ready for a deployment in the >January release. I've completed the changes for using the workspace >deluxe service and they are currently in a wsdeluxe branch in the git repo >for the module. I'm still waiting to hear when I should merge the branch >to master for the build. Please copy me and Matt Benedict on any >questions or help during the build. > >Mike Mundy | Senior Analyst Programmer | Bioinformatics >Systems Unit | 507-266-7232 | mundy.michael(a)mayo.edu >Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | mayoclinic.org ><http://www.mayoclinic.org> > > > > >On 12/16/13 12:17 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: > >>kbase devels, >> >>We will start a new release on Jan 6, the first day of the hack a thon at >>LBL. To start preparing, we need everyone to help by sending to Miriam >>when you think your module will be ready for a deployment. We have some >>deadlines to work towards, so lets start the relase process early. >> >>Miriam has agreed to take care of the overall tracking of the release >>process. She will be updating our lists and making sure communication >>works smoothly, so please give her your support if she reaches out to >>you. >> >>Also, consistent with previous builds, any modules that haven't been >>through at least one round of black box testing by the test team needs to >>be. Miriam will follow up on that front to. >> >> >>Thanks in advance, >>Tom >>_______________________________________________ >>Kbase-devel mailing list >>Kbase-devel(a)lists.kbase.us >>https://lists.kbase.us/mailman/listinfo/kbase-devel >

1 0

Build planning: "war room" and kickoff meeting [was Re: Do we have a plan for gettting things all together and deployed for the 15th.]
by Nomi Harris 05 Jan '14

05 Jan '14

Yes, we can make the KBase conference room the Build war room. Other (non-build-related) meetings can take place in the open area at KBase, or in the conference room at JBEI across the street (or in Adam's office if they're small meetings). Please see the new "Scheduled meetings" spreadsheet at https://docs.google.com/spreadsheet/ccc?key=0AmAQmB9wdNbZdGZfVVJrYzFkYjQ4cU… where I have listed the scheduled meetings and their locations. I can move more of the meetings scheduled for the "KBase open area" to JBEI if it turns out to be too disruptive to have those meetings in the open area. (However, the conference room at JBEI that we are using for the other meetings, JBEI 978-4111, is not available on Wednesday. I can check other conference rooms.) Gwyneth had scheduled a Build meeting on Wed. afternoon but I would like to move it to Mon @ 4pm. That's the first time when everyone relevant will have arrived and be available. (Of course, that doesn't mean that you can't talk to some of the people involved before that!) Does that time work for everyone? Nomi On Jan 4, 2014, at 5:15 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov> wrote: > Can we commandeer a deployment war room with a whiteboard, or is there no such room available? Having the small conference room just for the deployment team, with whiteboards with modules, dependencies, readiness, exceptional variations, etc would be useful.

1 0

Re: [Release-team] Do we have a plan for gettting things all together and deployed for the 15th.
by Shane Canon 05 Jan '14

05 Jan '14

Sure. We can discuss it tomorrow. Shane Sent from my iPhone > On Jan 4, 2014, at 5:56 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: > > Hey Shane, > > Can you take this on next week? See thread below. We can talk on Monday, and Rick could probably provide some scripts. > > Tom > > > On Jan 4, 2014, at 7:43 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov> > wrote: > >> I think having a small team, maybe led by Shane, that looks into this would be great. A team of two really would do it. One to run a ramped DoS sort of code, and another to monitor the stack (mysql , mongo, star man, nginx, memory, network gear, etc) >> >> Having this done in parallel to Bob's changes. If Bob can roll the changes in early, say as soon as he arrives, then all deployments would have the decaying retry capability. >> >> t >> >> >> On Jan 4, 2014, at 7:38 PM, "Rick @ Argonne" <stevens(a)anl.gov> >> wrote: >> >>> Tom >>> >>> As you know I'm also seeing reliably issues with some servers/services. Perhaps we need a dive on that. Bob thinks a modification to the client side code generator can support a smart retry that should improve things and be reflected in all clients. I'm also wondering if we have something configure to limit number of sever connections per client to foil denial of service attacks that might be causing some of this. ? >>> >>> Sent from my iPhone >>> >>> On Jan 4, 2014, at 19:15, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: >>> >>>> Right. When I was writing the messae, I was realizing there was going to be a phase two, someting beyond the 15th. As I was writing I wondered if i should discuss the two phases in the same email. What I describe is what we'll do, but not everything that we will do of course. >>>> >>>> Yes, the idea to whiteboard things is good. This will elicit the info needed to fully understand what the 'private' deployment will be. I need Dan and Shane present for that. >>>> >>>> Can we commandeer a deployment war room with a whiteboard, or is there no such room available? Having the small conference room just for the deployment team, with whiteboards with modules, dependencies, readiness, exceptional variations, etc would be useful. >>>> >>>> >>>> >>>> >>>> On Jan 4, 2014, at 6:56 PM, Adam Arkin <aparkin(a)lbl.gov> >>>> wrote: >>>> >>>>> Hi Tom , >>>>> >>>>> I wish we could enforce this... but in my speaking to the various teams I know there are going to be issues with meeting this deadline. The question right now is how to deal with this is an orderly way given that what you voice is the theoretically correct way... >>>>> >>>>> Search won't complete because not everyone has their types or data in the system yet, Landing pages and the attendant widgets are still in development, WSS is not complete for a variety reasons, and there are a few other elements that are not all there. >>>>> >>>>> I propose we need to, in the first couple of days next week, take over a big board in the conference room and try and get all the modules and their interdependencies onto the board, determine the elements ready and not for deployment, and then prioritize and assign names to the tasks for completion. >>>>> >>>>> Some links for docs that might be useful: >>>>> Narrative: http://kbase.us/docs/narrative/functions/index.html >>>>> >>>>> Workspace object format: https://docs.google.com/a/lbl.gov/document/d/1cFaSLxtW7QfsIhlreRko_AE_nRoLJ… >>>>> >>>>> Documentation of Widget making and landing pages: >>>> >>>> >>>>> >>>>> https://docs.google.com/a/lbl.gov/document/d/1Jwy9uIet1HoJcqjOgvyjYpJyFlIKV… >>>>> >>>>> This is a spreadsheet of indexed objects and whether or not they have landing pages: >>>>> https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AvN8PTXC3N8wdEVXdlBB… >>>>> >>>>> >>>>> So-- we need some way to phrase your message that says we need to get as much deployed by the 13th as possible and we will be accounting for and scheduling those elements that cannot make it because of missed dependencies. >>>>> >>>>> >>>>> Sigh... >>>>> >>>>> A >>>>> >>>>> >>>>>> On Sat, Jan 4, 2014 at 4:36 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov> wrote: >>>>>> Here is a draft announcement for the schedule for the deployments. Of course, the hard deadline for deployment to production is Jan 15. >>>>>> >>>>>> Builds are scheduled to take place from Jan 7-13, 2014. Activities will cease on the end of Jan 15 and at that time we will take inventory of what made it into production. The build pattern is mostly unchanged, module owners communicate to the release team modules that are ready. The release team deploys the module to the test environment, executes the tests, and then deploys the module to production. Triage based on failures occurs along the way, and module owners have the opportunity to fix problems and resubmit the module as ready to the release team. The release team will take no new deployment requests after Jan 13, so that the Jan 15 production deployment schedule can be kept. On Jan 16, a report to Adam will be compiled by the release team and submitted. >>>>>> >>>>>> On Monday, Jan 6, or as soon as a the release team arrives, the KBase services spread sheet will be finalized, and the build punchlist will be reviewed. >>>>>> >>>>>> Feedback welcome. I will send tomorrow or later this evening if Adam you are ok with this schedule. >>>>>> >>>>>> Tom >>>>>> >>>>>> >>>>>> >>>>>>> On Jan 3, 2014, at 1:19 PM, Adam Arkin <aparkin(a)lbl.gov> wrote: >>>>>>> >>>>>>> That would be great. We need to get a hard end to deploy. >>>>>>> Do we have a plan for a public vs. "private" instance? >>>>>>> >>>>>>> A >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On Fri, Jan 3, 2014 at 11:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: >>>>>>>> I can do a formal timeline for prod deploys. Would formally start on the 13th. of Jan.; after the hackathon, but we can start earlier on those that are ready. >>>>>>>> >>>>>>>> Would work out the logistics of tracking with Miriam, Nomi, Dan, Shane next week >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> On Jan 3, 2014, at 12:58 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: >>>>>>>>> >>>>>>>>> I can do a timeline for prod deploys. Would formally start >>>>>>>>> >>>>>>>>> Sent from my Verizon Wireless 4G LTE DROID >>>>>>>>> >>>>>>>>> >>>>>>>>> Adam Arkin <aparkin(a)lbl.gov> wrote: >>>>>>>>> >>>>>>>>> Hi All, >>>>>>>>> >>>>>>>>> I know already people are pushing the deadline... I am very worried about this. >>>>>>>>> If we are going to push the deadline we should do so formally and set the process for final deployment and testing. >>>>>>>>> >>>>>>>>> We also were going to have a public site and a site with more advanced functionality for friends. Is this going to happen? >>>>>>>>> >>>>>>>>> Should we get people on a schedule? How should we manage this? >>>>>>>>> >>>>>>>>> >>>>>>>>> A >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Adam Paul Arkin >>>>>>>>> Dean A. Richard Newton Memorial Chair >>>>>>>>> ------------------------------------- >>>>>>>>> Director, Physical Biosciences Division >>>>>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>>>>> >>>>>>>>> Professor, Department of Bioengineering >>>>>>>>> University of California >>>>>>>>> Berkeley, CA, 94720 >>>>>>>>> >>>>>>>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>>>>>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>>>>>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>>>>>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>>>>>>> >>>>>>>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>>>>>>> Mailing address: >>>>>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>>>>> 1 Cyclotron Road, MS 955-512L >>>>>>>>> Berkeley, CA 94720 >>>>>>>>> >>>>>>>>> Contact: >>>>>>>>> W: http://genomics.lbl.gov >>>>>>>>> V: 510-495-2366 >>>>>>>>> C: 510-206-1389 >>>>>>>>> F: 510-486-6219 >>>>>>>>> >>>>>>>>> Assistant: >>>>>>>>> Gwyneth A. Terry >>>>>>>>> V: 510-495-2116 >>>>>>>>> E: GATerry(a)lbl.gov >>>>>>>>> ------------------------------------- >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Adam Paul Arkin >>>>>>> Dean A. Richard Newton Memorial Chair >>>>>>> ------------------------------------- >>>>>>> Director, Physical Biosciences Division >>>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>>> >>>>>>> Professor, Department of Bioengineering >>>>>>> University of California >>>>>>> Berkeley, CA, 94720 >>>>>>> >>>>>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>>>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>>>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>>>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>>>>> >>>>>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>>>>> Mailing address: >>>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>>> 1 Cyclotron Road, MS 955-512L >>>>>>> Berkeley, CA 94720 >>>>>>> >>>>>>> Contact: >>>>>>> W: http://genomics.lbl.gov >>>>>>> V: 510-495-2366 >>>>>>> C: 510-206-1389 >>>>>>> F: 510-486-6219 >>>>>>> >>>>>>> Assistant: >>>>>>> Gwyneth A. Terry >>>>>>> V: 510-495-2116 >>>>>>> E: GATerry(a)lbl.gov >>>>>>> ------------------------------------- >>>>> >>>>> >>>>> >>>>> -- >>>>> Adam Paul Arkin >>>>> Dean A. Richard Newton Memorial Chair >>>>> ------------------------------------- >>>>> Director, Physical Biosciences Division >>>>> E.O. Lawrence Berkeley National Laboratory >>>>> >>>>> Professor, Department of Bioengineering >>>>> University of California >>>>> Berkeley, CA, 94720 >>>>> >>>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>>> >>>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>>> Mailing address: >>>>> E.O. Lawrence Berkeley National Laboratory >>>>> 1 Cyclotron Road, MS 955-512L >>>>> Berkeley, CA 94720 >>>>> >>>>> Contact: >>>>> W: http://genomics.lbl.gov >>>>> V: 510-495-2366 >>>>> C: 510-206-1389 >>>>> F: 510-486-6219 >>>>> >>>>> Assistant: >>>>> Gwyneth A. Terry >>>>> V: 510-495-2116 >>>>> E: GATerry(a)lbl.gov >>>>> ------------------------------------- >

1 0

Re: [Release-team] Do we have a plan for gettting things all together and deployed for the 15th.
by Brettin, Thomas S. 04 Jan '14

04 Jan '14

Hey Shane, Can you take this on next week? See thread below. We can talk on Monday, and Rick could probably provide some scripts. Tom On Jan 4, 2014, at 7:43 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]>> wrote: I think having a small team, maybe led by Shane, that looks into this would be great. A team of two really would do it. One to run a ramped DoS sort of code, and another to monitor the stack (mysql , mongo, star man, nginx, memory, network gear, etc) Having this done in parallel to Bob's changes. If Bob can roll the changes in early, say as soon as he arrives, then all deployments would have the decaying retry capability. t On Jan 4, 2014, at 7:38 PM, "Rick @ Argonne" <stevens(a)anl.gov<mailto:[email protected]>> wrote: Tom As you know I'm also seeing reliably issues with some servers/services. Perhaps we need a dive on that. Bob thinks a modification to the client side code generator can support a smart retry that should improve things and be reflected in all clients. I'm also wondering if we have something configure to limit number of sever connections per client to foil denial of service attacks that might be causing some of this. ? Sent from my iPhone On Jan 4, 2014, at 19:15, "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]>> wrote: Right. When I was writing the messae, I was realizing there was going to be a phase two, someting beyond the 15th. As I was writing I wondered if i should discuss the two phases in the same email. What I describe is what we'll do, but not everything that we will do of course. Yes, the idea to whiteboard things is good. This will elicit the info needed to fully understand what the 'private' deployment will be. I need Dan and Shane present for that. Can we commandeer a deployment war room with a whiteboard, or is there no such room available? Having the small conference room just for the deployment team, with whiteboards with modules, dependencies, readiness, exceptional variations, etc would be useful. On Jan 4, 2014, at 6:56 PM, Adam Arkin <aparkin(a)lbl.gov<mailto:[email protected]>> wrote: Hi Tom , I wish we could enforce this... but in my speaking to the various teams I know there are going to be issues with meeting this deadline. The question right now is how to deal with this is an orderly way given that what you voice is the theoretically correct way... Search won't complete because not everyone has their types or data in the system yet, Landing pages and the attendant widgets are still in development, WSS is not complete for a variety reasons, and there are a few other elements that are not all there. I propose we need to, in the first couple of days next week, take over a big board in the conference room and try and get all the modules and their interdependencies onto the board, determine the elements ready and not for deployment, and then prioritize and assign names to the tasks for completion. Some links for docs that might be useful: Narrative: http://kbase.us/docs/narrative/functions/index.html Workspace object format: https://docs.google.com/a/lbl.gov/document/d/1cFaSLxtW7QfsIhlreRko_AE_nRoLJ… Documentation of Widget making and landing pages: https://docs.google.com/a/lbl.gov/document/d/1Jwy9uIet1HoJcqjOgvyjYpJyFlIKV… This is a spreadsheet of indexed objects and whether or not they have landing pages: https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AvN8PTXC3N8wdEVXdlBB… So-- we need some way to phrase your message that says we need to get as much deployed by the 13th as possible and we will be accounting for and scheduling those elements that cannot make it because of missed dependencies. Sigh... A On Sat, Jan 4, 2014 at 4:36 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov<mailto:[email protected]>> wrote: Here is a draft announcement for the schedule for the deployments. Of course, the hard deadline for deployment to production is Jan 15. Builds are scheduled to take place from Jan 7-13, 2014. Activities will cease on the end of Jan 15 and at that time we will take inventory of what made it into production. The build pattern is mostly unchanged, module owners communicate to the release team modules that are ready. The release team deploys the module to the test environment, executes the tests, and then deploys the module to production. Triage based on failures occurs along the way, and module owners have the opportunity to fix problems and resubmit the module as ready to the release team. The release team will take no new deployment requests after Jan 13, so that the Jan 15 production deployment schedule can be kept. On Jan 16, a report to Adam will be compiled by the release team and submitted. On Monday, Jan 6, or as soon as a the release team arrives, the KBase services spread sheet will be finalized, and the build punchlist will be reviewed. Feedback welcome. I will send tomorrow or later this evening if Adam you are ok with this schedule. Tom On Jan 3, 2014, at 1:19 PM, Adam Arkin <aparkin(a)lbl.gov<mailto:[email protected]>> wrote: That would be great. We need to get a hard end to deploy. Do we have a plan for a public vs. "private" instance? A On Fri, Jan 3, 2014 at 11:05 AM, Thomas Brettin <brettint(a)gmail.com<mailto:[email protected]>> wrote: I can do a formal timeline for prod deploys. Would formally start on the 13th. of Jan.; after the hackathon, but we can start earlier on those that are ready. Would work out the logistics of tracking with Miriam, Nomi, Dan, Shane next week On Jan 3, 2014, at 12:58 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]>> wrote: I can do a timeline for prod deploys. Would formally start Sent from my Verizon Wireless 4G LTE DROID Adam Arkin <aparkin(a)lbl.gov<mailto:[email protected]>> wrote: Hi All, I know already people are pushing the deadline... I am very worried about this. If we are going to push the deadline we should do so formally and set the process for final deployment and testing. We also were going to have a public site and a site with more advanced functionality for friends. Is this going to happen? Should we get people on a schedule? How should we manage this? A -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us <http://kbase.us/> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu<http://synbio.berkeley.edu/> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov<http://vimss.lbl.gov/> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org<http://energybiosciencesinstitute.org/> Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov<http://genomics.lbl.gov/> V: 510-495-2366<tel:510-495-2366> C: 510-206-1389<tel:510-206-1389> F: 510-486-6219<tel:510-486-6219> Assistant: Gwyneth A. Terry V: 510-495-2116<tel:510-495-2116> E: GATerry(a)lbl.gov<mailto:[email protected]> ------------------------------------- -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us <http://kbase.us/> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu<http://synbio.berkeley.edu/> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov<http://vimss.lbl.gov/> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org<http://energybiosciencesinstitute.org/> Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov<http://genomics.lbl.gov/> V: 510-495-2366<tel:510-495-2366> C: 510-206-1389<tel:510-206-1389> F: 510-486-6219<tel:510-486-6219> Assistant: Gwyneth A. Terry V: 510-495-2116<tel:510-495-2116> E: GATerry(a)lbl.gov<mailto:[email protected]> ------------------------------------- -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us <http://kbase.us/> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu<http://synbio.berkeley.edu/> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov<http://vimss.lbl.gov/> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org<http://energybiosciencesinstitute.org/> Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov<http://genomics.lbl.gov/> V: 510-495-2366 C: 510-206-1389 F: 510-486-6219 Assistant: Gwyneth A. Terry V: 510-495-2116 E: GATerry(a)lbl.gov<mailto:[email protected]> -------------------------------------

1 0

Re: [Release-team] Do we have a plan for gettting things all together and deployed for the 15th.
by Adam Paul Arkin 04 Jan '14

04 Jan '14

Ha.. We can station someone on the visitor network at jbei. Please excuse any terseness or errors. This is sent from my mobile. -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO DOE Systems Biology Knowledgebase, http://kbase.us Director, Berkeley Synthetic Biology Institute,http://synbio.berkeley.edu PI and Co-director, Virtual Institute of Microbial Stress and Survival,http://vimss.lbl.gov Investigator, Energy Biosciences Institute,http://energybiosciencesinstitute.org Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov V: 510-495-2366 C: 510-206-1389 F: 510-486-6219 Assistant: Gwyneth A. Terry V: 510-495-2116 E: GATerry(a)lbl.gov ------------------------------------- > On Jan 4, 2014, at 5:52 PM, "Rick @ Argonne" <stevens(a)anl.gov> wrote: > > I agree its important that we test and understand the behavior a typical user will experience. And fix it if it's not what we want. > > Typical user? ==? running on a laptop on a so so network. ;-) > > Sent from my iPhone > >> On Jan 4, 2014, at 19:43, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: >> >> I think having a small team, maybe led by Shane, that looks into this would be great. A team of two really would do it. One to run a ramped DoS sort of code, and another to monitor the stack (mysql , mongo, star man, nginx, memory, network gear, etc) >> >> Having this done in parallel to Bob's changes. If Bob can roll the changes in early, say as soon as he arrives, then all deployments would have the decaying retry capability. >> >> t >> >> >> On Jan 4, 2014, at 7:38 PM, "Rick @ Argonne" <stevens(a)anl.gov> >> wrote: >> >>> Tom >>> >>> As you know I'm also seeing reliably issues with some servers/services. Perhaps we need a dive on that. Bob thinks a modification to the client side code generator can support a smart retry that should improve things and be reflected in all clients. I'm also wondering if we have something configure to limit number of sever connections per client to foil denial of service attacks that might be causing some of this. ? >>> >>> Sent from my iPhone >>> >>> On Jan 4, 2014, at 19:15, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: >>> >>>> Right. When I was writing the messae, I was realizing there was going to be a phase two, someting beyond the 15th. As I was writing I wondered if i should discuss the two phases in the same email. What I describe is what we'll do, but not everything that we will do of course. >>>> >>>> Yes, the idea to whiteboard things is good. This will elicit the info needed to fully understand what the 'private' deployment will be. I need Dan and Shane present for that. >>>> >>>> Can we commandeer a deployment war room with a whiteboard, or is there no such room available? Having the small conference room just for the deployment team, with whiteboards with modules, dependencies, readiness, exceptional variations, etc would be useful. >>>> >>>> >>>> >>>> >>>> On Jan 4, 2014, at 6:56 PM, Adam Arkin <aparkin(a)lbl.gov> >>>> wrote: >>>> >>>>> Hi Tom , >>>>> >>>>> I wish we could enforce this... but in my speaking to the various teams I know there are going to be issues with meeting this deadline. The question right now is how to deal with this is an orderly way given that what you voice is the theoretically correct way... >>>>> >>>>> Search won't complete because not everyone has their types or data in the system yet, Landing pages and the attendant widgets are still in development, WSS is not complete for a variety reasons, and there are a few other elements that are not all there. >>>>> >>>>> I propose we need to, in the first couple of days next week, take over a big board in the conference room and try and get all the modules and their interdependencies onto the board, determine the elements ready and not for deployment, and then prioritize and assign names to the tasks for completion. >>>>> >>>>> Some links for docs that might be useful: >>>>> Narrative: http://kbase.us/docs/narrative/functions/index.html >>>>> >>>>> Workspace object format: https://docs.google.com/a/lbl.gov/document/d/1cFaSLxtW7QfsIhlreRko_AE_nRoLJ… >>>>> >>>>> Documentation of Widget making and landing pages: >>>> >>>> >>>>> >>>>> https://docs.google.com/a/lbl.gov/document/d/1Jwy9uIet1HoJcqjOgvyjYpJyFlIKV… >>>>> >>>>> This is a spreadsheet of indexed objects and whether or not they have landing pages: >>>>> https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AvN8PTXC3N8wdEVXdlBB… >>>>> >>>>> >>>>> So-- we need some way to phrase your message that says we need to get as much deployed by the 13th as possible and we will be accounting for and scheduling those elements that cannot make it because of missed dependencies. >>>>> >>>>> >>>>> Sigh... >>>>> >>>>> A >>>>> >>>>> >>>>>> On Sat, Jan 4, 2014 at 4:36 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov> wrote: >>>>>> Here is a draft announcement for the schedule for the deployments. Of course, the hard deadline for deployment to production is Jan 15. >>>>>> >>>>>> Builds are scheduled to take place from Jan 7-13, 2014. Activities will cease on the end of Jan 15 and at that time we will take inventory of what made it into production. The build pattern is mostly unchanged, module owners communicate to the release team modules that are ready. The release team deploys the module to the test environment, executes the tests, and then deploys the module to production. Triage based on failures occurs along the way, and module owners have the opportunity to fix problems and resubmit the module as ready to the release team. The release team will take no new deployment requests after Jan 13, so that the Jan 15 production deployment schedule can be kept. On Jan 16, a report to Adam will be compiled by the release team and submitted. >>>>>> >>>>>> On Monday, Jan 6, or as soon as a the release team arrives, the KBase services spread sheet will be finalized, and the build punchlist will be reviewed. >>>>>> >>>>>> Feedback welcome. I will send tomorrow or later this evening if Adam you are ok with this schedule. >>>>>> >>>>>> Tom >>>>>> >>>>>> >>>>>> >>>>>>> On Jan 3, 2014, at 1:19 PM, Adam Arkin <aparkin(a)lbl.gov> wrote: >>>>>>> >>>>>>> That would be great. We need to get a hard end to deploy. >>>>>>> Do we have a plan for a public vs. "private" instance? >>>>>>> >>>>>>> A >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On Fri, Jan 3, 2014 at 11:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: >>>>>>>> I can do a formal timeline for prod deploys. Would formally start on the 13th. of Jan.; after the hackathon, but we can start earlier on those that are ready. >>>>>>>> >>>>>>>> Would work out the logistics of tracking with Miriam, Nomi, Dan, Shane next week >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>>> On Jan 3, 2014, at 12:58 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: >>>>>>>>> >>>>>>>>> I can do a timeline for prod deploys. Would formally start >>>>>>>>> >>>>>>>>> Sent from my Verizon Wireless 4G LTE DROID >>>>>>>>> >>>>>>>>> >>>>>>>>> Adam Arkin <aparkin(a)lbl.gov> wrote: >>>>>>>>> >>>>>>>>> Hi All, >>>>>>>>> >>>>>>>>> I know already people are pushing the deadline... I am very worried about this. >>>>>>>>> If we are going to push the deadline we should do so formally and set the process for final deployment and testing. >>>>>>>>> >>>>>>>>> We also were going to have a public site and a site with more advanced functionality for friends. Is this going to happen? >>>>>>>>> >>>>>>>>> Should we get people on a schedule? How should we manage this? >>>>>>>>> >>>>>>>>> >>>>>>>>> A >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Adam Paul Arkin >>>>>>>>> Dean A. Richard Newton Memorial Chair >>>>>>>>> ------------------------------------- >>>>>>>>> Director, Physical Biosciences Division >>>>>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>>>>> >>>>>>>>> Professor, Department of Bioengineering >>>>>>>>> University of California >>>>>>>>> Berkeley, CA, 94720 >>>>>>>>> >>>>>>>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>>>>>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>>>>>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>>>>>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>>>>>>> >>>>>>>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>>>>>>> Mailing address: >>>>>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>>>>> 1 Cyclotron Road, MS 955-512L >>>>>>>>> Berkeley, CA 94720 >>>>>>>>> >>>>>>>>> Contact: >>>>>>>>> W: http://genomics.lbl.gov >>>>>>>>> V: 510-495-2366 >>>>>>>>> C: 510-206-1389 >>>>>>>>> F: 510-486-6219 >>>>>>>>> >>>>>>>>> Assistant: >>>>>>>>> Gwyneth A. Terry >>>>>>>>> V: 510-495-2116 >>>>>>>>> E: GATerry(a)lbl.gov >>>>>>>>> ------------------------------------- >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Adam Paul Arkin >>>>>>> Dean A. Richard Newton Memorial Chair >>>>>>> ------------------------------------- >>>>>>> Director, Physical Biosciences Division >>>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>>> >>>>>>> Professor, Department of Bioengineering >>>>>>> University of California >>>>>>> Berkeley, CA, 94720 >>>>>>> >>>>>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>>>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>>>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>>>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>>>>> >>>>>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>>>>> Mailing address: >>>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>>> 1 Cyclotron Road, MS 955-512L >>>>>>> Berkeley, CA 94720 >>>>>>> >>>>>>> Contact: >>>>>>> W: http://genomics.lbl.gov >>>>>>> V: 510-495-2366 >>>>>>> C: 510-206-1389 >>>>>>> F: 510-486-6219 >>>>>>> >>>>>>> Assistant: >>>>>>> Gwyneth A. Terry >>>>>>> V: 510-495-2116 >>>>>>> E: GATerry(a)lbl.gov >>>>>>> ------------------------------------- >>>>> >>>>> >>>>> >>>>> -- >>>>> Adam Paul Arkin >>>>> Dean A. Richard Newton Memorial Chair >>>>> ------------------------------------- >>>>> Director, Physical Biosciences Division >>>>> E.O. Lawrence Berkeley National Laboratory >>>>> >>>>> Professor, Department of Bioengineering >>>>> University of California >>>>> Berkeley, CA, 94720 >>>>> >>>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>>> >>>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>>> Mailing address: >>>>> E.O. Lawrence Berkeley National Laboratory >>>>> 1 Cyclotron Road, MS 955-512L >>>>> Berkeley, CA 94720 >>>>> >>>>> Contact: >>>>> W: http://genomics.lbl.gov >>>>> V: 510-495-2366 >>>>> C: 510-206-1389 >>>>> F: 510-486-6219 >>>>> >>>>> Assistant: >>>>> Gwyneth A. Terry >>>>> V: 510-495-2116 >>>>> E: GATerry(a)lbl.gov >>>>> ------------------------------------- >>

1 0

Re: [Release-team] Do we have a plan for gettting things all together and deployed for the 15th.
by Rick ＠ Argonne 04 Jan '14

04 Jan '14

I agree its important that we test and understand the behavior a typical user will experience. And fix it if it's not what we want. Typical user? ==? running on a laptop on a so so network. ;-) Sent from my iPhone > On Jan 4, 2014, at 19:43, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: > > I think having a small team, maybe led by Shane, that looks into this would be great. A team of two really would do it. One to run a ramped DoS sort of code, and another to monitor the stack (mysql , mongo, star man, nginx, memory, network gear, etc) > > Having this done in parallel to Bob's changes. If Bob can roll the changes in early, say as soon as he arrives, then all deployments would have the decaying retry capability. > > t > > > On Jan 4, 2014, at 7:38 PM, "Rick @ Argonne" <stevens(a)anl.gov> > wrote: > >> Tom >> >> As you know I'm also seeing reliably issues with some servers/services. Perhaps we need a dive on that. Bob thinks a modification to the client side code generator can support a smart retry that should improve things and be reflected in all clients. I'm also wondering if we have something configure to limit number of sever connections per client to foil denial of service attacks that might be causing some of this. ? >> >> Sent from my iPhone >> >> On Jan 4, 2014, at 19:15, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: >> >>> Right. When I was writing the messae, I was realizing there was going to be a phase two, someting beyond the 15th. As I was writing I wondered if i should discuss the two phases in the same email. What I describe is what we'll do, but not everything that we will do of course. >>> >>> Yes, the idea to whiteboard things is good. This will elicit the info needed to fully understand what the 'private' deployment will be. I need Dan and Shane present for that. >>> >>> Can we commandeer a deployment war room with a whiteboard, or is there no such room available? Having the small conference room just for the deployment team, with whiteboards with modules, dependencies, readiness, exceptional variations, etc would be useful. >>> >>> >>> >>> >>> On Jan 4, 2014, at 6:56 PM, Adam Arkin <aparkin(a)lbl.gov> >>> wrote: >>> >>>> Hi Tom , >>>> >>>> I wish we could enforce this... but in my speaking to the various teams I know there are going to be issues with meeting this deadline. The question right now is how to deal with this is an orderly way given that what you voice is the theoretically correct way... >>>> >>>> Search won't complete because not everyone has their types or data in the system yet, Landing pages and the attendant widgets are still in development, WSS is not complete for a variety reasons, and there are a few other elements that are not all there. >>>> >>>> I propose we need to, in the first couple of days next week, take over a big board in the conference room and try and get all the modules and their interdependencies onto the board, determine the elements ready and not for deployment, and then prioritize and assign names to the tasks for completion. >>>> >>>> Some links for docs that might be useful: >>>> Narrative: http://kbase.us/docs/narrative/functions/index.html >>>> >>>> Workspace object format: https://docs.google.com/a/lbl.gov/document/d/1cFaSLxtW7QfsIhlreRko_AE_nRoLJ… >>>> >>>> Documentation of Widget making and landing pages: >>> >>> >>>> >>>> https://docs.google.com/a/lbl.gov/document/d/1Jwy9uIet1HoJcqjOgvyjYpJyFlIKV… >>>> >>>> This is a spreadsheet of indexed objects and whether or not they have landing pages: >>>> https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AvN8PTXC3N8wdEVXdlBB… >>>> >>>> >>>> So-- we need some way to phrase your message that says we need to get as much deployed by the 13th as possible and we will be accounting for and scheduling those elements that cannot make it because of missed dependencies. >>>> >>>> >>>> Sigh... >>>> >>>> A >>>> >>>> >>>>> On Sat, Jan 4, 2014 at 4:36 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov> wrote: >>>>> Here is a draft announcement for the schedule for the deployments. Of course, the hard deadline for deployment to production is Jan 15. >>>>> >>>>> Builds are scheduled to take place from Jan 7-13, 2014. Activities will cease on the end of Jan 15 and at that time we will take inventory of what made it into production. The build pattern is mostly unchanged, module owners communicate to the release team modules that are ready. The release team deploys the module to the test environment, executes the tests, and then deploys the module to production. Triage based on failures occurs along the way, and module owners have the opportunity to fix problems and resubmit the module as ready to the release team. The release team will take no new deployment requests after Jan 13, so that the Jan 15 production deployment schedule can be kept. On Jan 16, a report to Adam will be compiled by the release team and submitted. >>>>> >>>>> On Monday, Jan 6, or as soon as a the release team arrives, the KBase services spread sheet will be finalized, and the build punchlist will be reviewed. >>>>> >>>>> Feedback welcome. I will send tomorrow or later this evening if Adam you are ok with this schedule. >>>>> >>>>> Tom >>>>> >>>>> >>>>> >>>>>> On Jan 3, 2014, at 1:19 PM, Adam Arkin <aparkin(a)lbl.gov> wrote: >>>>>> >>>>>> That would be great. We need to get a hard end to deploy. >>>>>> Do we have a plan for a public vs. "private" instance? >>>>>> >>>>>> A >>>>>> >>>>>> >>>>>> >>>>>>> On Fri, Jan 3, 2014 at 11:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: >>>>>>> I can do a formal timeline for prod deploys. Would formally start on the 13th. of Jan.; after the hackathon, but we can start earlier on those that are ready. >>>>>>> >>>>>>> Would work out the logistics of tracking with Miriam, Nomi, Dan, Shane next week >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> On Jan 3, 2014, at 12:58 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: >>>>>>>> >>>>>>>> I can do a timeline for prod deploys. Would formally start >>>>>>>> >>>>>>>> Sent from my Verizon Wireless 4G LTE DROID >>>>>>>> >>>>>>>> >>>>>>>> Adam Arkin <aparkin(a)lbl.gov> wrote: >>>>>>>> >>>>>>>> Hi All, >>>>>>>> >>>>>>>> I know already people are pushing the deadline... I am very worried about this. >>>>>>>> If we are going to push the deadline we should do so formally and set the process for final deployment and testing. >>>>>>>> >>>>>>>> We also were going to have a public site and a site with more advanced functionality for friends. Is this going to happen? >>>>>>>> >>>>>>>> Should we get people on a schedule? How should we manage this? >>>>>>>> >>>>>>>> >>>>>>>> A >>>>>>>> >>>>>>>> -- >>>>>>>> Adam Paul Arkin >>>>>>>> Dean A. Richard Newton Memorial Chair >>>>>>>> ------------------------------------- >>>>>>>> Director, Physical Biosciences Division >>>>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>>>> >>>>>>>> Professor, Department of Bioengineering >>>>>>>> University of California >>>>>>>> Berkeley, CA, 94720 >>>>>>>> >>>>>>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>>>>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>>>>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>>>>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>>>>>> >>>>>>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>>>>>> Mailing address: >>>>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>>>> 1 Cyclotron Road, MS 955-512L >>>>>>>> Berkeley, CA 94720 >>>>>>>> >>>>>>>> Contact: >>>>>>>> W: http://genomics.lbl.gov >>>>>>>> V: 510-495-2366 >>>>>>>> C: 510-206-1389 >>>>>>>> F: 510-486-6219 >>>>>>>> >>>>>>>> Assistant: >>>>>>>> Gwyneth A. Terry >>>>>>>> V: 510-495-2116 >>>>>>>> E: GATerry(a)lbl.gov >>>>>>>> ------------------------------------- >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Adam Paul Arkin >>>>>> Dean A. Richard Newton Memorial Chair >>>>>> ------------------------------------- >>>>>> Director, Physical Biosciences Division >>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>> >>>>>> Professor, Department of Bioengineering >>>>>> University of California >>>>>> Berkeley, CA, 94720 >>>>>> >>>>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>>>> >>>>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>>>> Mailing address: >>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>> 1 Cyclotron Road, MS 955-512L >>>>>> Berkeley, CA 94720 >>>>>> >>>>>> Contact: >>>>>> W: http://genomics.lbl.gov >>>>>> V: 510-495-2366 >>>>>> C: 510-206-1389 >>>>>> F: 510-486-6219 >>>>>> >>>>>> Assistant: >>>>>> Gwyneth A. Terry >>>>>> V: 510-495-2116 >>>>>> E: GATerry(a)lbl.gov >>>>>> ------------------------------------- >>>> >>>> >>>> >>>> -- >>>> Adam Paul Arkin >>>> Dean A. Richard Newton Memorial Chair >>>> ------------------------------------- >>>> Director, Physical Biosciences Division >>>> E.O. Lawrence Berkeley National Laboratory >>>> >>>> Professor, Department of Bioengineering >>>> University of California >>>> Berkeley, CA, 94720 >>>> >>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>> >>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>> Mailing address: >>>> E.O. Lawrence Berkeley National Laboratory >>>> 1 Cyclotron Road, MS 955-512L >>>> Berkeley, CA 94720 >>>> >>>> Contact: >>>> W: http://genomics.lbl.gov >>>> V: 510-495-2366 >>>> C: 510-206-1389 >>>> F: 510-486-6219 >>>> >>>> Assistant: >>>> Gwyneth A. Terry >>>> V: 510-495-2116 >>>> E: GATerry(a)lbl.gov >>>> ------------------------------------- >

1 0

Re: [Release-team] Do we have a plan for gettting things all together and deployed for the 15th.
by Brettin, Thomas S. 04 Jan '14

04 Jan '14

I think having a small team, maybe led by Shane, that looks into this would be great. A team of two really would do it. One to run a ramped DoS sort of code, and another to monitor the stack (mysql , mongo, star man, nginx, memory, network gear, etc) Having this done in parallel to Bob's changes. If Bob can roll the changes in early, say as soon as he arrives, then all deployments would have the decaying retry capability. t On Jan 4, 2014, at 7:38 PM, "Rick @ Argonne" <stevens(a)anl.gov<mailto:[email protected]>> wrote: Tom As you know I'm also seeing reliably issues with some servers/services. Perhaps we need a dive on that. Bob thinks a modification to the client side code generator can support a smart retry that should improve things and be reflected in all clients. I'm also wondering if we have something configure to limit number of sever connections per client to foil denial of service attacks that might be causing some of this. ? Sent from my iPhone On Jan 4, 2014, at 19:15, "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]>> wrote: Right. When I was writing the messae, I was realizing there was going to be a phase two, someting beyond the 15th. As I was writing I wondered if i should discuss the two phases in the same email. What I describe is what we'll do, but not everything that we will do of course. Yes, the idea to whiteboard things is good. This will elicit the info needed to fully understand what the 'private' deployment will be. I need Dan and Shane present for that. Can we commandeer a deployment war room with a whiteboard, or is there no such room available? Having the small conference room just for the deployment team, with whiteboards with modules, dependencies, readiness, exceptional variations, etc would be useful. On Jan 4, 2014, at 6:56 PM, Adam Arkin <aparkin(a)lbl.gov<mailto:[email protected]>> wrote: Hi Tom , I wish we could enforce this... but in my speaking to the various teams I know there are going to be issues with meeting this deadline. The question right now is how to deal with this is an orderly way given that what you voice is the theoretically correct way... Search won't complete because not everyone has their types or data in the system yet, Landing pages and the attendant widgets are still in development, WSS is not complete for a variety reasons, and there are a few other elements that are not all there. I propose we need to, in the first couple of days next week, take over a big board in the conference room and try and get all the modules and their interdependencies onto the board, determine the elements ready and not for deployment, and then prioritize and assign names to the tasks for completion. Some links for docs that might be useful: Narrative: http://kbase.us/docs/narrative/functions/index.html Workspace object format: https://docs.google.com/a/lbl.gov/document/d/1cFaSLxtW7QfsIhlreRko_AE_nRoLJ… Documentation of Widget making and landing pages: https://docs.google.com/a/lbl.gov/document/d/1Jwy9uIet1HoJcqjOgvyjYpJyFlIKV… This is a spreadsheet of indexed objects and whether or not they have landing pages: https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AvN8PTXC3N8wdEVXdlBB… So-- we need some way to phrase your message that says we need to get as much deployed by the 13th as possible and we will be accounting for and scheduling those elements that cannot make it because of missed dependencies. Sigh... A On Sat, Jan 4, 2014 at 4:36 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov<mailto:[email protected]>> wrote: Here is a draft announcement for the schedule for the deployments. Of course, the hard deadline for deployment to production is Jan 15. Builds are scheduled to take place from Jan 7-13, 2014. Activities will cease on the end of Jan 15 and at that time we will take inventory of what made it into production. The build pattern is mostly unchanged, module owners communicate to the release team modules that are ready. The release team deploys the module to the test environment, executes the tests, and then deploys the module to production. Triage based on failures occurs along the way, and module owners have the opportunity to fix problems and resubmit the module as ready to the release team. The release team will take no new deployment requests after Jan 13, so that the Jan 15 production deployment schedule can be kept. On Jan 16, a report to Adam will be compiled by the release team and submitted. On Monday, Jan 6, or as soon as a the release team arrives, the KBase services spread sheet will be finalized, and the build punchlist will be reviewed. Feedback welcome. I will send tomorrow or later this evening if Adam you are ok with this schedule. Tom On Jan 3, 2014, at 1:19 PM, Adam Arkin <aparkin(a)lbl.gov<mailto:[email protected]>> wrote: That would be great. We need to get a hard end to deploy. Do we have a plan for a public vs. "private" instance? A On Fri, Jan 3, 2014 at 11:05 AM, Thomas Brettin <brettint(a)gmail.com<mailto:[email protected]>> wrote: I can do a formal timeline for prod deploys. Would formally start on the 13th. of Jan.; after the hackathon, but we can start earlier on those that are ready. Would work out the logistics of tracking with Miriam, Nomi, Dan, Shane next week On Jan 3, 2014, at 12:58 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov<mailto:[email protected]>> wrote: I can do a timeline for prod deploys. Would formally start Sent from my Verizon Wireless 4G LTE DROID Adam Arkin <aparkin(a)lbl.gov<mailto:[email protected]>> wrote: Hi All, I know already people are pushing the deadline... I am very worried about this. If we are going to push the deadline we should do so formally and set the process for final deployment and testing. We also were going to have a public site and a site with more advanced functionality for friends. Is this going to happen? Should we get people on a schedule? How should we manage this? A -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us <http://kbase.us/> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu<http://synbio.berkeley.edu/> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov<http://vimss.lbl.gov/> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org<http://energybiosciencesinstitute.org/> Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov<http://genomics.lbl.gov/> V: 510-495-2366<tel:510-495-2366> C: 510-206-1389<tel:510-206-1389> F: 510-486-6219<tel:510-486-6219> Assistant: Gwyneth A. Terry V: 510-495-2116<tel:510-495-2116> E: GATerry(a)lbl.gov<mailto:[email protected]> ------------------------------------- -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us <http://kbase.us/> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu<http://synbio.berkeley.edu/> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov<http://vimss.lbl.gov/> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org<http://energybiosciencesinstitute.org/> Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov<http://genomics.lbl.gov/> V: 510-495-2366<tel:510-495-2366> C: 510-206-1389<tel:510-206-1389> F: 510-486-6219<tel:510-486-6219> Assistant: Gwyneth A. Terry V: 510-495-2116<tel:510-495-2116> E: GATerry(a)lbl.gov<mailto:[email protected]> ------------------------------------- -- Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us <http://kbase.us/> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu<http://synbio.berkeley.edu/> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov<http://vimss.lbl.gov/> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org<http://energybiosciencesinstitute.org/> Office: 512C Energy Biosciences Building (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS 955-512L Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov<http://genomics.lbl.gov/> V: 510-495-2366 C: 510-206-1389 F: 510-486-6219 Assistant: Gwyneth A. Terry V: 510-495-2116 E: GATerry(a)lbl.gov<mailto:[email protected]> -------------------------------------

1 0

Re: [Release-team] Do we have a plan for gettting things all together and deployed for the 15th.
by Rick ＠ Argonne 04 Jan '14

04 Jan '14

Tom As you know I'm also seeing reliably issues with some servers/services. Perhaps we need a dive on that. Bob thinks a modification to the client side code generator can support a smart retry that should improve things and be reflected in all clients. I'm also wondering if we have something configure to limit number of sever connections per client to foil denial of service attacks that might be causing some of this. ? Sent from my iPhone > On Jan 4, 2014, at 19:15, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: > > Right. When I was writing the messae, I was realizing there was going to be a phase two, someting beyond the 15th. As I was writing I wondered if i should discuss the two phases in the same email. What I describe is what we'll do, but not everything that we will do of course. > > Yes, the idea to whiteboard things is good. This will elicit the info needed to fully understand what the 'private' deployment will be. I need Dan and Shane present for that. > > Can we commandeer a deployment war room with a whiteboard, or is there no such room available? Having the small conference room just for the deployment team, with whiteboards with modules, dependencies, readiness, exceptional variations, etc would be useful. > > > > > On Jan 4, 2014, at 6:56 PM, Adam Arkin <aparkin(a)lbl.gov> > wrote: > >> Hi Tom , >> >> I wish we could enforce this... but in my speaking to the various teams I know there are going to be issues with meeting this deadline. The question right now is how to deal with this is an orderly way given that what you voice is the theoretically correct way... >> >> Search won't complete because not everyone has their types or data in the system yet, Landing pages and the attendant widgets are still in development, WSS is not complete for a variety reasons, and there are a few other elements that are not all there. >> >> I propose we need to, in the first couple of days next week, take over a big board in the conference room and try and get all the modules and their interdependencies onto the board, determine the elements ready and not for deployment, and then prioritize and assign names to the tasks for completion. >> >> Some links for docs that might be useful: >> Narrative: http://kbase.us/docs/narrative/functions/index.html >> >> Workspace object format: https://docs.google.com/a/lbl.gov/document/d/1cFaSLxtW7QfsIhlreRko_AE_nRoLJ… >> >> Documentation of Widget making and landing pages: > > >> >> https://docs.google.com/a/lbl.gov/document/d/1Jwy9uIet1HoJcqjOgvyjYpJyFlIKV… >> >> This is a spreadsheet of indexed objects and whether or not they have landing pages: >> https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AvN8PTXC3N8wdEVXdlBB… >> >> >> So-- we need some way to phrase your message that says we need to get as much deployed by the 13th as possible and we will be accounting for and scheduling those elements that cannot make it because of missed dependencies. >> >> >> Sigh... >> >> A >> >> >>> On Sat, Jan 4, 2014 at 4:36 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov> wrote: >>> Here is a draft announcement for the schedule for the deployments. Of course, the hard deadline for deployment to production is Jan 15. >>> >>> Builds are scheduled to take place from Jan 7-13, 2014. Activities will cease on the end of Jan 15 and at that time we will take inventory of what made it into production. The build pattern is mostly unchanged, module owners communicate to the release team modules that are ready. The release team deploys the module to the test environment, executes the tests, and then deploys the module to production. Triage based on failures occurs along the way, and module owners have the opportunity to fix problems and resubmit the module as ready to the release team. The release team will take no new deployment requests after Jan 13, so that the Jan 15 production deployment schedule can be kept. On Jan 16, a report to Adam will be compiled by the release team and submitted. >>> >>> On Monday, Jan 6, or as soon as a the release team arrives, the KBase services spread sheet will be finalized, and the build punchlist will be reviewed. >>> >>> Feedback welcome. I will send tomorrow or later this evening if Adam you are ok with this schedule. >>> >>> Tom >>> >>> >>> >>>> On Jan 3, 2014, at 1:19 PM, Adam Arkin <aparkin(a)lbl.gov> wrote: >>>> >>>> That would be great. We need to get a hard end to deploy. >>>> Do we have a plan for a public vs. "private" instance? >>>> >>>> A >>>> >>>> >>>> >>>>> On Fri, Jan 3, 2014 at 11:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: >>>>> I can do a formal timeline for prod deploys. Would formally start on the 13th. of Jan.; after the hackathon, but we can start earlier on those that are ready. >>>>> >>>>> Would work out the logistics of tracking with Miriam, Nomi, Dan, Shane next week >>>>> >>>>> >>>>> >>>>> >>>>>> On Jan 3, 2014, at 12:58 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: >>>>>> >>>>>> I can do a timeline for prod deploys. Would formally start >>>>>> >>>>>> Sent from my Verizon Wireless 4G LTE DROID >>>>>> >>>>>> >>>>>> Adam Arkin <aparkin(a)lbl.gov> wrote: >>>>>> >>>>>> Hi All, >>>>>> >>>>>> I know already people are pushing the deadline... I am very worried about this. >>>>>> If we are going to push the deadline we should do so formally and set the process for final deployment and testing. >>>>>> >>>>>> We also were going to have a public site and a site with more advanced functionality for friends. Is this going to happen? >>>>>> >>>>>> Should we get people on a schedule? How should we manage this? >>>>>> >>>>>> >>>>>> A >>>>>> >>>>>> -- >>>>>> Adam Paul Arkin >>>>>> Dean A. Richard Newton Memorial Chair >>>>>> ------------------------------------- >>>>>> Director, Physical Biosciences Division >>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>> >>>>>> Professor, Department of Bioengineering >>>>>> University of California >>>>>> Berkeley, CA, 94720 >>>>>> >>>>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>>>> >>>>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>>>> Mailing address: >>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>> 1 Cyclotron Road, MS 955-512L >>>>>> Berkeley, CA 94720 >>>>>> >>>>>> Contact: >>>>>> W: http://genomics.lbl.gov >>>>>> V: 510-495-2366 >>>>>> C: 510-206-1389 >>>>>> F: 510-486-6219 >>>>>> >>>>>> Assistant: >>>>>> Gwyneth A. Terry >>>>>> V: 510-495-2116 >>>>>> E: GATerry(a)lbl.gov >>>>>> ------------------------------------- >>>> >>>> >>>> >>>> -- >>>> Adam Paul Arkin >>>> Dean A. Richard Newton Memorial Chair >>>> ------------------------------------- >>>> Director, Physical Biosciences Division >>>> E.O. Lawrence Berkeley National Laboratory >>>> >>>> Professor, Department of Bioengineering >>>> University of California >>>> Berkeley, CA, 94720 >>>> >>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>> >>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>> Mailing address: >>>> E.O. Lawrence Berkeley National Laboratory >>>> 1 Cyclotron Road, MS 955-512L >>>> Berkeley, CA 94720 >>>> >>>> Contact: >>>> W: http://genomics.lbl.gov >>>> V: 510-495-2366 >>>> C: 510-206-1389 >>>> F: 510-486-6219 >>>> >>>> Assistant: >>>> Gwyneth A. Terry >>>> V: 510-495-2116 >>>> E: GATerry(a)lbl.gov >>>> ------------------------------------- >> >> >> >> -- >> Adam Paul Arkin >> Dean A. Richard Newton Memorial Chair >> ------------------------------------- >> Director, Physical Biosciences Division >> E.O. Lawrence Berkeley National Laboratory >> >> Professor, Department of Bioengineering >> University of California >> Berkeley, CA, 94720 >> >> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >> >> Office: 512C Energy Biosciences Building (Berkeley Campus) >> Mailing address: >> E.O. Lawrence Berkeley National Laboratory >> 1 Cyclotron Road, MS 955-512L >> Berkeley, CA 94720 >> >> Contact: >> W: http://genomics.lbl.gov >> V: 510-495-2366 >> C: 510-206-1389 >> F: 510-486-6219 >> >> Assistant: >> Gwyneth A. Terry >> V: 510-495-2116 >> E: GATerry(a)lbl.gov >> ------------------------------------- >

1 0

Re: [Release-team] Do we have a plan for gettting things all together and deployed for the 15th.
by Rick ＠ Argonne 04 Jan '14

04 Jan '14

Good plan Tom. I agree some place to war room the attack is needed. Sent from my iPhone > On Jan 4, 2014, at 19:15, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: > > Right. When I was writing the messae, I was realizing there was going to be a phase two, someting beyond the 15th. As I was writing I wondered if i should discuss the two phases in the same email. What I describe is what we'll do, but not everything that we will do of course. > > Yes, the idea to whiteboard things is good. This will elicit the info needed to fully understand what the 'private' deployment will be. I need Dan and Shane present for that. > > Can we commandeer a deployment war room with a whiteboard, or is there no such room available? Having the small conference room just for the deployment team, with whiteboards with modules, dependencies, readiness, exceptional variations, etc would be useful. > > > > > On Jan 4, 2014, at 6:56 PM, Adam Arkin <aparkin(a)lbl.gov> > wrote: > >> Hi Tom , >> >> I wish we could enforce this... but in my speaking to the various teams I know there are going to be issues with meeting this deadline. The question right now is how to deal with this is an orderly way given that what you voice is the theoretically correct way... >> >> Search won't complete because not everyone has their types or data in the system yet, Landing pages and the attendant widgets are still in development, WSS is not complete for a variety reasons, and there are a few other elements that are not all there. >> >> I propose we need to, in the first couple of days next week, take over a big board in the conference room and try and get all the modules and their interdependencies onto the board, determine the elements ready and not for deployment, and then prioritize and assign names to the tasks for completion. >> >> Some links for docs that might be useful: >> Narrative: http://kbase.us/docs/narrative/functions/index.html >> >> Workspace object format: https://docs.google.com/a/lbl.gov/document/d/1cFaSLxtW7QfsIhlreRko_AE_nRoLJ… >> >> Documentation of Widget making and landing pages: > > >> >> https://docs.google.com/a/lbl.gov/document/d/1Jwy9uIet1HoJcqjOgvyjYpJyFlIKV… >> >> This is a spreadsheet of indexed objects and whether or not they have landing pages: >> https://docs.google.com/a/lbl.gov/spreadsheet/ccc?key=0AvN8PTXC3N8wdEVXdlBB… >> >> >> So-- we need some way to phrase your message that says we need to get as much deployed by the 13th as possible and we will be accounting for and scheduling those elements that cannot make it because of missed dependencies. >> >> >> Sigh... >> >> A >> >> >>> On Sat, Jan 4, 2014 at 4:36 PM, Brettin, Thomas S. <brettin(a)cels.anl.gov> wrote: >>> Here is a draft announcement for the schedule for the deployments. Of course, the hard deadline for deployment to production is Jan 15. >>> >>> Builds are scheduled to take place from Jan 7-13, 2014. Activities will cease on the end of Jan 15 and at that time we will take inventory of what made it into production. The build pattern is mostly unchanged, module owners communicate to the release team modules that are ready. The release team deploys the module to the test environment, executes the tests, and then deploys the module to production. Triage based on failures occurs along the way, and module owners have the opportunity to fix problems and resubmit the module as ready to the release team. The release team will take no new deployment requests after Jan 13, so that the Jan 15 production deployment schedule can be kept. On Jan 16, a report to Adam will be compiled by the release team and submitted. >>> >>> On Monday, Jan 6, or as soon as a the release team arrives, the KBase services spread sheet will be finalized, and the build punchlist will be reviewed. >>> >>> Feedback welcome. I will send tomorrow or later this evening if Adam you are ok with this schedule. >>> >>> Tom >>> >>> >>> >>>> On Jan 3, 2014, at 1:19 PM, Adam Arkin <aparkin(a)lbl.gov> wrote: >>>> >>>> That would be great. We need to get a hard end to deploy. >>>> Do we have a plan for a public vs. "private" instance? >>>> >>>> A >>>> >>>> >>>> >>>>> On Fri, Jan 3, 2014 at 11:05 AM, Thomas Brettin <brettint(a)gmail.com> wrote: >>>>> I can do a formal timeline for prod deploys. Would formally start on the 13th. of Jan.; after the hackathon, but we can start earlier on those that are ready. >>>>> >>>>> Would work out the logistics of tracking with Miriam, Nomi, Dan, Shane next week >>>>> >>>>> >>>>> >>>>> >>>>>> On Jan 3, 2014, at 12:58 PM, "Brettin, Thomas S." <brettin(a)cels.anl.gov> wrote: >>>>>> >>>>>> I can do a timeline for prod deploys. Would formally start >>>>>> >>>>>> Sent from my Verizon Wireless 4G LTE DROID >>>>>> >>>>>> >>>>>> Adam Arkin <aparkin(a)lbl.gov> wrote: >>>>>> >>>>>> Hi All, >>>>>> >>>>>> I know already people are pushing the deadline... I am very worried about this. >>>>>> If we are going to push the deadline we should do so formally and set the process for final deployment and testing. >>>>>> >>>>>> We also were going to have a public site and a site with more advanced functionality for friends. Is this going to happen? >>>>>> >>>>>> Should we get people on a schedule? How should we manage this? >>>>>> >>>>>> >>>>>> A >>>>>> >>>>>> -- >>>>>> Adam Paul Arkin >>>>>> Dean A. Richard Newton Memorial Chair >>>>>> ------------------------------------- >>>>>> Director, Physical Biosciences Division >>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>> >>>>>> Professor, Department of Bioengineering >>>>>> University of California >>>>>> Berkeley, CA, 94720 >>>>>> >>>>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>>>> >>>>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>>>> Mailing address: >>>>>> E.O. Lawrence Berkeley National Laboratory >>>>>> 1 Cyclotron Road, MS 955-512L >>>>>> Berkeley, CA 94720 >>>>>> >>>>>> Contact: >>>>>> W: http://genomics.lbl.gov >>>>>> V: 510-495-2366 >>>>>> C: 510-206-1389 >>>>>> F: 510-486-6219 >>>>>> >>>>>> Assistant: >>>>>> Gwyneth A. Terry >>>>>> V: 510-495-2116 >>>>>> E: GATerry(a)lbl.gov >>>>>> ------------------------------------- >>>> >>>> >>>> >>>> -- >>>> Adam Paul Arkin >>>> Dean A. Richard Newton Memorial Chair >>>> ------------------------------------- >>>> Director, Physical Biosciences Division >>>> E.O. Lawrence Berkeley National Laboratory >>>> >>>> Professor, Department of Bioengineering >>>> University of California >>>> Berkeley, CA, 94720 >>>> >>>> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >>>> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >>>> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >>>> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >>>> >>>> Office: 512C Energy Biosciences Building (Berkeley Campus) >>>> Mailing address: >>>> E.O. Lawrence Berkeley National Laboratory >>>> 1 Cyclotron Road, MS 955-512L >>>> Berkeley, CA 94720 >>>> >>>> Contact: >>>> W: http://genomics.lbl.gov >>>> V: 510-495-2366 >>>> C: 510-206-1389 >>>> F: 510-486-6219 >>>> >>>> Assistant: >>>> Gwyneth A. Terry >>>> V: 510-495-2116 >>>> E: GATerry(a)lbl.gov >>>> ------------------------------------- >> >> >> >> -- >> Adam Paul Arkin >> Dean A. Richard Newton Memorial Chair >> ------------------------------------- >> Director, Physical Biosciences Division >> E.O. Lawrence Berkeley National Laboratory >> >> Professor, Department of Bioengineering >> University of California >> Berkeley, CA, 94720 >> >> CEO/CSO, DOE Systems Biology Knowledgebase, http://kbase.us >> Director, Berkeley Synthetic Biology Institute, http://synbio.berkeley.edu >> PI and Co-Director, ENIGMA SFA, http://enigma.lbl.gov >> Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org >> >> Office: 512C Energy Biosciences Building (Berkeley Campus) >> Mailing address: >> E.O. Lawrence Berkeley National Laboratory >> 1 Cyclotron Road, MS 955-512L >> Berkeley, CA 94720 >> >> Contact: >> W: http://genomics.lbl.gov >> V: 510-495-2366 >> C: 510-206-1389 >> F: 510-486-6219 >> >> Assistant: >> Gwyneth A. Terry >> V: 510-495-2116 >> E: GATerry(a)lbl.gov >> ------------------------------------- >

1 0