Menu
▾
▴
pipeline130-developers — Developer Mailing List
You can subscribe to this list here.
| 2009 |
Jan
|
Feb
|
Mar
|
Apr
(37) |
May
(113) |
Jun
(62) |
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|---|
|
From: <cs...@uc...> - 2009-04-25 02:44:56
|
Our plan for getting this all done by Monday: everybody keep editing the wiki like last time. Only this time we really need participation from everyone... I know I am going to be very very busy this weekend and I have to make the powerpoint, too. The design doc page is linked to from the main wiki page and I've already added a bit to it. Please feel free to totally change what I have -- I just threw stuff up so we have a starting point. In order to gear up for development (which should start SOON), please everybody try to set up your Java dev environment. I personally recommend NetBeans, a full-featured IDE a lot like Visual Studio. It runs on Windows, OS X and Linux. Here's what I added to the meetings page: Design doc/presentation plans: Chris will present on Monday, everybody needs to add to wiki page. General consensus is that we need to focus our energy (both in the design and implementation stages) on the Workflow Engine and one single Workflow Manager implementation, probably the console app. The GUI editor should probably be our lowest priority, since we can hand-craft the workflow documents. Key things to nail down soon are the Engine application design, the Manager<->Engine communication protocol, and the Workflow XML schema. Anything we come up with can definitely change, but we need something for Monday for sure. The design for the Engine should take into account what the DRMAA interface offers us. This page looks like it has a decent summary of using DRMAA: [1] PLEASE EDIT THE WIKI, even if what you write does not belong in the 'formal' document. If need be, we can always move it to a new page. Quoting Nils Homer <nil...@uc...>: > Sorry I missed the meeting, I have not been feeling well. Could someone > update me on what was discussed (i.e. Post it on the wiki meetings section) > and how we are going to get the "design" section done this Monday? > > Nils > > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensign option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > Pipeline130-developers mailing list > Pip...@li... > https://lists.sourceforge.net/lists/listinfo/pipeline130-developers > |
|
From: Nils H. <nil...@uc...> - 2009-04-24 20:16:47
|
Sorry I missed the meeting, I have not been feeling well. Could someone update me on what was discussed (i.e. Post it on the wiki meetings section) and how we are going to get the "design" section done this Monday? Nils |
|
From: Mike H. <mh...@uc...> - 2009-04-20 17:15:48
|
Yep looks good to me. -Mike On Apr 20, 2009, at 10:09 AM, Nils Homer wrote: > Looks like we have a few ppl putting together the final doc. Since > Chris > has it in a pdf, we can upload that one. Are all of you ok with that? > Chris, can you upload it to courseweb? > > Nils > > > On 4/20/09 12:28 AM, "Chris Swan" <cs...@uc...> wrote: > >> Since nobody else is up for it... >> >> Attached are a PDF and .doc copy of the document based off the >> latest copy >> on the wiki. It's not perfect, but I'm comfortable handing it in. I >> don't >> think they'll read it particularly carefully anyway. >> >> -Chris >> >> -------------------------------------------------- >> From: "Nils Homer" <nil...@uc...> >> Sent: Sunday, April 19, 2009 10:26 PM >> To: <pip...@li...> >> Subject: [Pipeline130-developers] Requirements doc >> >>> Does someone want to take the information on the requirements wiki >>> page >>> and >>> convert it to a word/latex/ doc etc? We can then have a final >>> revision >>> (send it around) and then we can convert it to pdf (unless already >>> in that >>> form) for upload in the AM? >>> >>> Please respond if you want to take the lead on this. This is a >>> good time >>> to >>> catch up for those who haven't contributed. >>> >>> Nils >>> >>> >>> >>> > -----------------------------------------------------------------------------> > > > - >>> Stay on top of everything new and different, both inside and >>> around Java (TM) technology - register by April 22, and save >>> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. >>> 300 plus technical and hands-on sessions. Register today. >>> Use priority code J9JMT32. http://p.sf.net/sfu/p >>> _______________________________________________ >>> Pipeline130-developers mailing list >>> Pip...@li... >>> https://lists.sourceforge.net/lists/listinfo/pipeline130-developers >>> > > > > ------------------------------------------------------------------------------ > Stay on top of everything new and different, both inside and > around Java (TM) technology - register by April 22, and save > $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. > 300 plus technical and hands-on sessions. Register today. > Use priority code J9JMT32. http://p.sf.net/sfu/p > _______________________________________________ > Pipeline130-developers mailing list > Pip...@li... > https://lists.sourceforge.net/lists/listinfo/pipeline130-developers |
|
From: Chris S. <cs...@uc...> - 2009-04-20 17:15:44
|
Submitted. -Chris -------------------------------------------------- From: "Nils Homer" <nil...@uc...> Sent: Monday, April 20, 2009 10:09 AM To: "Chris Swan" <cs...@uc...>; <pip...@li...> Subject: Re: [Pipeline130-developers] Requirements doc > Looks like we have a few ppl putting together the final doc. Since Chris > has it in a pdf, we can upload that one. Are all of you ok with that? > Chris, can you upload it to courseweb? > > Nils > > > On 4/20/09 12:28 AM, "Chris Swan" <cs...@uc...> wrote: > >> Since nobody else is up for it... >> >> Attached are a PDF and .doc copy of the document based off the latest >> copy >> on the wiki. It's not perfect, but I'm comfortable handing it in. I don't >> think they'll read it particularly carefully anyway. >> >> -Chris >> >> -------------------------------------------------- >> From: "Nils Homer" <nil...@uc...> >> Sent: Sunday, April 19, 2009 10:26 PM >> To: <pip...@li...> >> Subject: [Pipeline130-developers] Requirements doc >> >>> Does someone want to take the information on the requirements wiki page >>> and >>> convert it to a word/latex/ doc etc? We can then have a final revision >>> (send it around) and then we can convert it to pdf (unless already in >>> that >>> form) for upload in the AM? >>> >>> Please respond if you want to take the lead on this. This is a good >>> time >>> to >>> catch up for those who haven't contributed. >>> >>> Nils >>> >>> >>> >>> > ----------------------------------------------------------------------------->> > - >>> Stay on top of everything new and different, both inside and >>> around Java (TM) technology - register by April 22, and save >>> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. >>> 300 plus technical and hands-on sessions. Register today. >>> Use priority code J9JMT32. http://p.sf.net/sfu/p >>> _______________________________________________ >>> Pipeline130-developers mailing list >>> Pip...@li... >>> https://lists.sourceforge.net/lists/listinfo/pipeline130-developers >>> > > > |
|
From: Nils H. <nil...@uc...> - 2009-04-20 17:10:17
|
Looks like we have a few ppl putting together the final doc. Since Chris has it in a pdf, we can upload that one. Are all of you ok with that? Chris, can you upload it to courseweb? Nils On 4/20/09 12:28 AM, "Chris Swan" <cs...@uc...> wrote: > Since nobody else is up for it... > > Attached are a PDF and .doc copy of the document based off the latest copy > on the wiki. It's not perfect, but I'm comfortable handing it in. I don't > think they'll read it particularly carefully anyway. > > -Chris > > -------------------------------------------------- > From: "Nils Homer" <nil...@uc...> > Sent: Sunday, April 19, 2009 10:26 PM > To: <pip...@li...> > Subject: [Pipeline130-developers] Requirements doc > >> Does someone want to take the information on the requirements wiki page >> and >> convert it to a word/latex/ doc etc? We can then have a final revision >> (send it around) and then we can convert it to pdf (unless already in that >> form) for upload in the AM? >> >> Please respond if you want to take the lead on this. This is a good time >> to >> catch up for those who haven't contributed. >> >> Nils >> >> >> >> ----------------------------------------------------------------------------->> - >> Stay on top of everything new and different, both inside and >> around Java (TM) technology - register by April 22, and save >> $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. >> 300 plus technical and hands-on sessions. Register today. >> Use priority code J9JMT32. http://p.sf.net/sfu/p >> _______________________________________________ >> Pipeline130-developers mailing list >> Pip...@li... >> https://lists.sourceforge.net/lists/listinfo/pipeline130-developers >> |
|
From: Chris S. <cs...@uc...> - 2009-04-20 07:28:53
|
Since nobody else is up for it... Attached are a PDF and .doc copy of the document based off the latest copy on the wiki. It's not perfect, but I'm comfortable handing it in. I don't think they'll read it particularly carefully anyway. -Chris -------------------------------------------------- From: "Nils Homer" <nil...@uc...> Sent: Sunday, April 19, 2009 10:26 PM To: <pip...@li...> Subject: [Pipeline130-developers] Requirements doc > Does someone want to take the information on the requirements wiki page > and > convert it to a word/latex/ doc etc? We can then have a final revision > (send it around) and then we can convert it to pdf (unless already in that > form) for upload in the AM? > > Please respond if you want to take the lead on this. This is a good time > to > catch up for those who haven't contributed. > > Nils > > > > ------------------------------------------------------------------------------ > Stay on top of everything new and different, both inside and > around Java (TM) technology - register by April 22, and save > $200 on the JavaOne (SM) conference, June 2-5, 2009, San Francisco. > 300 plus technical and hands-on sessions. Register today. > Use priority code J9JMT32. http://p.sf.net/sfu/p > _______________________________________________ > Pipeline130-developers mailing list > Pip...@li... > https://lists.sourceforge.net/lists/listinfo/pipeline130-developers > |
|
From: Nils H. <nil...@uc...> - 2009-04-20 05:27:09
|
Does someone want to take the information on the requirements wiki page and convert it to a word/latex/ doc etc? We can then have a final revision (send it around) and then we can convert it to pdf (unless already in that form) for upload in the AM? Please respond if you want to take the lead on this. This is a good time to catch up for those who haven't contributed. Nils |
|
From: Nils H. <nil...@uc...> - 2009-04-19 21:06:48
|
Check the previous emails. You have the same rights as I do. Go do the ³features² page and find the wiki feature. Click on ³grant admin², Nils On 4/19/09 2:00 PM, "SeokWon Heo" <co...@uc...> wrote: > Hey. Nils > > Can you give permission? > I do not have permission to edit pages. > > I can see following reason. > ³The action you have requested is limited to users in one of the groups, > admin.² > > Thank you. > > // SeokWon Heo > > > > From: Nils Homer [mailto:nil...@uc...] > Sent: Sunday, April 19, 2009 1:01 PM > To: SeokWon Heo > Cc: pip...@li... > Subject: Re: CS130 Meeting Times > > Can you add this to the wiki please? It would good practice since you need to > edit the wiki to contribute ot the req docs > > Nils > > > On 4/19/09 12:47 PM, "SeokWon Heo" <co...@uc...> wrote: > Hi~! > This is SeokWon Heo. > > Sorry for late response. > > I cannot edit the wiki. > So, Can you enter my schedule? > > MON : 10AM-2PM > TUE : 10AM-12PM, 4PM-6PM > WED : 10AM-2PM, 4PM-6PM > THU : 10AM-12PM, 4PM-6PM > FRI : 12PM-2PM > > Thank you. > > // SeokWon Heo > > |
|
From: Nils H. <nil...@uc...> - 2009-04-19 20:01:52
|
Can you add this to the wiki please? It would good practice since you need to edit the wiki to contribute ot the req docs Nils On 4/19/09 12:47 PM, "SeokWon Heo" <co...@uc...> wrote: > Hi~! > This is SeokWon Heo. > > Sorry for late response. > > I cannot edit the wiki. > So, Can you enter my schedule? > > MON : 10AM-2PM > TUE : 10AM-12PM, 4PM-6PM > WED : 10AM-2PM, 4PM-6PM > THU : 10AM-12PM, 4PM-6PM > FRI : 12PM-2PM > > Thank you. > > // SeokWon Heo > |
|
From: <cs...@uc...> - 2009-04-18 03:57:45
|
Hey guys, I just messed around in Visio and came up with what I think is a good representation of what we brainstormed in discussion today: https://apps.sourceforge.net/mediawiki/pipeline130/index.php?title=Image:Cs130_drawing1.png I will be putting the actual Visio file up on SVN sometime this weekend (when I'm home). If you've never used it before, it makes stuff like this really, really easy. You can access it through Remote Desktop to Seasnet : http://www.seas.ucla.edu/seasnet/remote/ . It's under Start->Programs->Microsoft Office. You can then save your diagram as a .png and upload it through the wiki software. Please ask if you need help! Also, consider giving it a shot and try to make lower-level versions of the one I did -- for example, expand one of the boxes like "Workflow Manager" into another diagram. If you're not up to that, try at least describing a diagram that's already up. I've embedded this image into the specification page ( https://apps.sourceforge.net/mediawiki/pipeline130/index.php?title=Requirements_document#Specification ), so you can just write about it there. Hopefully I/others will continue to add more as the weekend progresses and we'll have a nice spec by the end of it. -Chris |
|
From: Mike H. <mh...@uc...> - 2009-04-17 19:37:15
|
> This is a reply email from my family friend who works with this kind > of stuff at stanford if it helps. > > Mike Hess > > Begin forwarded message: > > >> Not only do I know Stan Nelson, but I'm doing a lot of work on >> next generation sequencing data. So you're definitely barking up >> the right tree. >> >> These machines are generating about 5-6 TB of data every three >> days. The big challenge is dealing with the volume of data -- the >> data being generated are large and most biological research sites >> are unprepared to deal with it because (1) they don't have the >> computational machinery, (2) they don't employ people who can >> operate the machinery, (3) data need to be moved to one place to >> another for processing (4) biologists have a long tradition of >> holding onto primary data, which is completely impractical in this >> case. >> >> Here's what happens: >> >> 1) biologists in the lab generate DNA samples that need to be >> sequenced >> 2) the biologist him/herself or a person running the sequencing >> machine sets up a bunch of parallel runs (can be more than one >> sample or can be multiple runs of the same sample) >> 3) after a couple days, each run produces a big image file (this >> is the 6TB). These data are usually only saved a few days. >> 4) the image files are analyzed to produce sequences with a >> quality score (usually FASTQ files) -- we call these the "reads". >> The length of the reads are a result of the technology being used, >> but are in general pretty short. These data are usually archived. >> 5) each individual read is aligned to a reference genome using one >> of a bunch of tools -- each has its advantages and disadvantages. >> 6) The aligned sequences will provide researchers with some >> information about the genome being sequenced -- usually it will be >> further analyzed with a pretty specific goal. >> >> What Stan is after is some way to keep track of each sequencing >> project, from the time it hits one of the sequencing machines >> through the standard steps of data analysis and the more customized >> steps. Your tool will have to be able to say where in this >> pipeline a project is, record the parameters of each machine/ >> analysis tool in the pipeline, produce reports and raw data from >> each step of the pipeline and be accessible via the internet. >> Because this is science, new analysis tools, new data formats, >> quality metrics, measurements etc will be developed on a daily >> basis. Your software architecture needs to be flexible enough that >> new features can be added easily and quickly. The interface needs >> to allow a very smart biologist to do exactly what they need to do >> without a big overhead of learning your system. >> >> Below, I've copied some stuff for you to look at. >> >> >> >> >> (1) from http://www.genengnews.com/articles/chitem.aspx?aid=2449 >> >> Each next-generation sequencer is unique in terms of the volume and >> nature of the data it generates over time and is greatly affected >> by how the instrument is used. Generally, purchasers of $0.5–2 mil >> lion instruments intend to operate it at near full capacity, gener >> ating anywhere from 600 GB (gigabytes) to 6 TB (terabytes) of data >> per run over a period of one to three days per run. >> >> One terabyte of data is not large by today’s standards. An externa >> l terabyte disk can be purchased for less than a few hundred dolla >> rs at any office supply store. Accumulating one terabyte per day, >> maintaining it for rapid online access, and archiving it for perma >> nent storage is a familiar problem to the sequencing center and ma >> ybe even the core facility, but this is a novel problem for the sm >> all research group and individual principal investigator. >> >> I have observed data being copied daily onto $300 external 1 TB USB >> drives and stacked high upon shelves. At the opposite extreme, I >> have also seen the implementation of six-figure, highly scalable, >> cluster file systems that are automatically replicated to a remote, >> off-site mirror for disaster recovery and automatically archived to >> tape using robotic tape libraries for permanent storage. Which is >> right? What do I recommend? >> >> Still by far, the least expensive and most reliable method of >> storing massive volumes of DNA sequence data is within a DNA >> molecule, and I’m only being somewhat flippant in reminding the re >> ader of this fact. The correct solution, though, is site-and use s >> pecific. >> >> If you were to compare the cost of a six-figure storage system to a >> few thousand dollars in biological reagents and a day’s instrument >> time, repeating an experiment is both a plausible and prudent mea >> ns of recovering lost sequence data. >> >> Researchers are resistant to discarding any data, however, they are >> accustomed to repeating experiments when necessary. An instrument’ >> s one terabyte per day of data consists of 90% primary, binary ima >> ge data that doesn’t compress well and 10% secondary, text sequenc >> e and meta-data (quality scores and alignment annotations) that co >> mpresses well. The primary data is needed in at least two cases. >> >> In the event the analysis algorithms change and improve, the user >> might want to reprocess primary data using updated software. Or, if >> an error is found in how the analysis was performed, the user might >> want to reprocess primary data with the same software but different >> parameters. >> >> These instruments, their corresponding software, and their use are >> so new that events requiring the reprocessing of primary data aren >> ’t entirely unlikely. If you’re willing to repeat experiments >> should adverse events occur, you can reduce the need for storage b >> y a factor of ten. >> >> >> >> from http://www.genomeweb.com/sequencing/core-labs-embrace-next-gen- >> sequencing-informatics-challenges-loom-large >> >> Data-Management Challenges >> >> Among core facilities that already own next-generation sequencers, >> data handling appears to be the greatest challenge. “The biggest c >> oncern of our sequencing core director at the moment is how to man >> age (annotate, store, retrieve, etc.) all of the data coming off t >> he instrument,” Chris Schad, a program manager for seven core geno >> mics-related laboratories at Mayo Clinic, told In Sequence by e-ma >> il. Mayo’s sequencing lab just took delivery of an Illumina Genome >> Analyzer, he said. >> >> Grills echoed the need for “significant informatics support.” >> His center has had an Illumina sequencer for several months and re >> cently returned a 454 sequencer after a demo period. The center is >> currently exploring ways to bring back the 454 instrument. >> >> “We deal with a lot of non-typical plant and animal model systems >> that have no reference sequence, so it’s extremely important to ha >> ve the [long read] capabilities that the 454 confers,” he said. >> >> One topic of discussion, he said, was the question of how long to >> store the raw sequencing data. “I think everybody agreed that the >> current paradigm is really, ‘you save all raw data.’ That might >> change over time, but right now, a core would typically have at le >> ast some kind of backup of data.” >> >> The main reasons are that samples may be irreplaceable, or users >> might want to take a second look at their data with new algorithms >> . “It reminds me very much of the early days of microarrays ... wh >> ere folks might want to reanalyze their raw data to get more infor >> mation out of it,” said Grills, whose center decided to back up al >> l of its next-gen sequencing data for the first year with a plan t >> o reevaluate its storage strategy at that time. >> >> Also, because the technology is so new, core facilities have to >> help develop applications and analysis tools. “There are really ve >> ry few standard protocols” for new sequencing applications like RN >> A profiling or ChIP sequencing, Grills said, and “the manufacturer >> s provide usable but not optimal tools [for informatics analysis], >> so we have to really compare and help develop new tools.” >> >> In addition, core facilities have to put up with “frequent upgrade >> s to hardware and software,” he said, making standardized operatin >> g protocols and quality metrics difficult to achieve. >> >> Another challenge is the need to schedule full runs and collect >> appropriate samples for them, he said, in order to run the >> instruments cost-efficiently. >> >> Core facilities also have to decide in what form to return the data >> to their customers. If they analyze data for them, they need to be >> aware that the large datasets take “a lot of time to analyze, even >> with the largest clusters,” Grills said. >> >> “Inevitably, the next-gen sequencing community will evolve the nec >> essary tools to make this process more routine and manageable ... >> but in the meantime, core labs will need to be prepared with exper >> tise to help design experiments and analyze data for many of their >> clients,” Steen said. >> |
|
From: <cs...@uc...> - 2009-04-17 02:16:32
|
Hi Brian and Jordan, My name is Chris and I'm in Nils' group for our CS130 project. I wasn't able to come to the meeting on Monday, but hopefully I will get to meet with you soon. As you might know, we're supposed to have a formal requirements and specifications document written by Monday. I think it would be nice if we could have an example of one or two of your actual workflows so that we can better nail down what exactly our system needs to support. I'm not very familiar with how your system works right now, so if that request doesn't really make sense, I apologize. Thanks a lot for your help! -Chris |
|
From: Nils H. <nil...@uc...> - 2009-04-15 07:22:35
|
No problem, I am giving a brief presentation tomorrow. Get your self on the pipeline mailing list, post your schedule on the wiki, and lets catch up after class tomorrow, Nils On 4/15/09 12:11 AM, "Kenny Wong" <nak...@ho...> wrote: > Hey Nils, > > This is Kenny Wong, I'm in your project group for CS130. I'm not sure if you > got my last email but, can you add me to the project on sourceforge (username > wongken)? I apologize for missing any meetings we may have had, but do you > mind filling me in on the presentation tomorrow? > > Thanks, > Kenny > >> > Date: Tue, 14 Apr 2009 23:15:00 -0700 >> > From: nil...@uc... >> > To: mh...@uc... >> > CC: pip...@li... >> > Subject: Re: [Pipeline130-developers] Presentation v1 >> > >> > We could just use an existing solution for the GUI, and adapt it for our >> > purposes. See Kepler. >> > >> > We are all going to have to learn to use the command line in Unix. Let me >> > know if this is a problem, and I can help you out learning the shell. >> > >> > Nils >> > >> > >> > On 4/14/09 10:26 PM, "Mike Hess" <mh...@uc...> wrote: >> > >>> > > Looks good. By the way is the GUI environment going to be for macs or >>> > > what? (I noticed it was for a unix environment.) >>> > > >>> > > -Mike >>> > > >>> > > On Apr 14, 2009, at 8:10 PM, Nils Homer wrote: >>> > > >>>> > >> Could you take a look over the presentation (attached). If there is >>>> > >> anything you want to add feel free and let me know so I can >>>> > >> incorporate it >>>> > >> by the am. >>>> > >> >>>> > >> You might have seen the email I sent to the prof. We might only >>>> > >> have a few >>>> > >> (5) people in the group so instead of building something from >>>> > >> scratch, we >>>> > >> could patch together a bunch of available software to get something >>>> > >> working. >>>> > >> Take a look at other software to see what you think. >>>> > >> >>>> > >> SeokWon, we don't have your schedule. >>>> > >> >>>> > >> Nils >>>> > >> >>>> > >> <Presentation - Project 7 - April 15 >>>> > >> 2009 >>>> > >> .v1 >>>> > >> .ppt >>>>> > >>> >>>> > >> >> > >> ----------------------------------------------------------------------------->> >> >> > - >>>> > >> This SF.net email is sponsored by: >>>> > >> High Quality Requirements in a Collaborative Environment. >>>> > >> Download a free trial of Rational Requirements Composer Now! >>>> > >> >>> > >>> >">http://p.sf.net/sfu/www-ibm-com__________________________________________ >>> ____>> >>> <http://p.sf.net/sfu/www-ibm-com____________________________________________>>> __> >> > _ >>>> > >> Pipeline130-developers mailing list >>>> > >> Pip...@li... >>>> > >> https://lists.sourceforge.net/lists/listinfo/pipeline130-developers >>> > > >> > >> > >> > >> > >> ------------------------------------------------------------------------------ >> > This SF.net email is sponsored by: >> > High Quality Requirements in a Collaborative Environment. >> > Download a free trial of Rational Requirements Composer Now! >> > http://p.sf.net/sfu/www-ibm-com >> > _______________________________________________ >> > Pipeline130-developers mailing list >> > Pip...@li... >> > https://lists.sourceforge.net/lists/listinfo/pipeline130-developers > > > Windows Live: Keep your life in sync. Check it out. > <http://windowslive.com/explore?ocid=TXT_TAGLM_WL_allup_1a_explore_042009> |
|
From: Nils H. <nil...@uc...> - 2009-04-15 06:15:28
|
We could just use an existing solution for the GUI, and adapt it for our purposes. See Kepler. We are all going to have to learn to use the command line in Unix. Let me know if this is a problem, and I can help you out learning the shell. Nils On 4/14/09 10:26 PM, "Mike Hess" <mh...@uc...> wrote: > Looks good. By the way is the GUI environment going to be for macs or > what? (I noticed it was for a unix environment.) > > -Mike > > On Apr 14, 2009, at 8:10 PM, Nils Homer wrote: > >> Could you take a look over the presentation (attached). If there is >> anything you want to add feel free and let me know so I can >> incorporate it >> by the am. >> >> You might have seen the email I sent to the prof. We might only >> have a few >> (5) people in the group so instead of building something from >> scratch, we >> could patch together a bunch of available software to get something >> working. >> Take a look at other software to see what you think. >> >> SeokWon, we don't have your schedule. >> >> Nils >> >> <Presentation - Project 7 - April 15 >> 2009 >> .v1 >> .ppt >>> >> ----------------------------------------------------------------------------->> - >> This SF.net email is sponsored by: >> High Quality Requirements in a Collaborative Environment. >> Download a free trial of Rational Requirements Composer Now! >> http://p.sf.net/sfu/www-ibm-com______________________________________________>> _ >> Pipeline130-developers mailing list >> Pip...@li... >> https://lists.sourceforge.net/lists/listinfo/pipeline130-developers > |
|
From: Mike H. <mh...@uc...> - 2009-04-15 05:27:47
|
Looks good. By the way is the GUI environment going to be for macs or what? (I noticed it was for a unix environment.) -Mike On Apr 14, 2009, at 8:10 PM, Nils Homer wrote: > Could you take a look over the presentation (attached). If there is > anything you want to add feel free and let me know so I can > incorporate it > by the am. > > You might have seen the email I sent to the prof. We might only > have a few > (5) people in the group so instead of building something from > scratch, we > could patch together a bunch of available software to get something > working. > Take a look at other software to see what you think. > > SeokWon, we don't have your schedule. > > Nils > > <Presentation - Project 7 - April 15 > 2009 > .v1 > .ppt > > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > High Quality Requirements in a Collaborative Environment. > Download a free trial of Rational Requirements Composer Now! > http://p.sf.net/sfu/www-ibm-com_______________________________________________ > Pipeline130-developers mailing list > Pip...@li... > https://lists.sourceforge.net/lists/listinfo/pipeline130-developers |
|
From: <cs...@uc...> - 2009-04-15 04:40:25
|
Looks good... just so you know, some of the pictures don't show up for me in Office 2007 for Windows (missing Quicktime decompressor). You might want to submit a PDF version. Quoting Nils Homer <nil...@uc...>: > Could you take a look over the presentation (attached). If there is > anything you want to add feel free and let me know so I can incorporate it > by the am. > > You might have seen the email I sent to the prof. We might only have a few > (5) people in the group so instead of building something from scratch, we > could patch together a bunch of available software to get something working. > Take a look at other software to see what you think. > > SeokWon, we don't have your schedule. > > Nils > > |
|
From: <cs...@uc...> - 2009-04-15 03:12:53
|
Nils, do you need/want any help with the powerpoint or any more talking points/slide content/etc? Quoting cs...@uc...: > I started a basic outline for the talk on Wednesday: > https://apps.sourceforge.net/mediawiki/pipeline130/index.php?title=Requirements#Presentation > > I figure each of the bullet points can be expanded to 1-2 slides. It's > very vague at the moment but it would be nice if everyone could pitch > in at least some small changes or ideas. As Nils said in his last > email, if you aren't able to edit the wiki, email the list and we can > update it for you. > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by: > High Quality Requirements in a Collaborative Environment. > Download a free trial of Rational Requirements Composer Now! > http://p.sf.net/sfu/www-ibm-com > _______________________________________________ > Pipeline130-developers mailing list > Pip...@li... > https://lists.sourceforge.net/lists/listinfo/pipeline130-developers > |
|
From: Nils H. <nil...@uc...> - 2009-04-15 03:12:00
|
Could you take a look over the presentation (attached). If there is anything you want to add feel free and let me know so I can incorporate it by the am. You might have seen the email I sent to the prof. We might only have a few (5) people in the group so instead of building something from scratch, we could patch together a bunch of available software to get something working. Take a look at other software to see what you think. SeokWon, we don't have your schedule. Nils |
|
From: Rupak M. <ru...@CS...> - 2009-04-14 05:29:15
|
On Mon, 13 Apr 2009, Nils Homer wrote: > Professor Rupak, > > I am the contact for Project 7 and we have not been able to contact via > email or in class (Friday or Monday) the following two project members. I > looked up their email via the UCLA directory. > > Tasinga, Penn > > and > > Wong, Kenny > > They may have dropped the class, be sick, or some other reason. How should > we proceed given we have only 5 reachable members? I will write to them. If they are not available, please attempt to re-write your requirements/scope of work for something suitable for 5. > > Finally, we met with the customers today and they mentioned instead of > writing something from scratch, they wouldn't mind seeing a software that is > composed of the best pieces of currently available tools, since they think > this will get a more polished and advanced project by the end of the > quarter. How do I respond to such a suggestion, or is it even acceptable, > give our impression that we are to design and build everything from scratch? I am happy if you build on top of existing infrastructure. In fact, I strongly suggest you use whatever is available. You can still design your part from scratch (eg show how what you'll bui.ld will fit into the existing design). Rupak > > Sincerely, > > Nils > > > ------ Forwarded Message >> From: Nils Homer <nil...@uc...> >> Date: Mon, 13 Apr 2009 10:04:03 -0700 >> To: <pta...@uc...>, <nak...@ho...> >> Conversation: CS 130 Project >> Subject: CS 130 Project >> >> Hey Guys, >> >> You are assigned to Project 7. Please check the cs130 website for a >> description of our project. We are going to meet with the customers after >> class today (mon april 13). >> >> Please also set up a SF account, join the following project and its developers >> mailing list asap. >> https://sourceforge.net/projects/pipeline130/ >> >> Nils > > ------ End of Forwarded Message > > -- Rupak Majumdar Associate Professor, Department of Computer Science University of California, Los Angeles, CA 90095 |
|
From: <cs...@uc...> - 2009-04-14 02:02:17
|
I started a basic outline for the talk on Wednesday: https://apps.sourceforge.net/mediawiki/pipeline130/index.php?title=Requirements#Presentation I figure each of the bullet points can be expanded to 1-2 slides. It's very vague at the moment but it would be nice if everyone could pitch in at least some small changes or ideas. As Nils said in his last email, if you aren't able to edit the wiki, email the list and we can update it for you. |
|
From: Nils H. <nil...@uc...> - 2009-04-14 00:41:55
|
Please add to the wiki what times you ARE NOT available: https://apps.sourceforge.net/mediawiki/pipeline130/index.php?title=Schedules If you don't know how to edit the wiki, send me the times and I will enter them in. Then the next meeting we can go over how to use wikis etc. Nils |
|
From: Nils H. <nil...@uc...> - 2009-04-13 22:59:41
|
Meeting notes can be found at: https://apps.sourceforge.net/mediawiki/pipeline130/index.php?title=Meetings Please read the notes as well as familiarizing yourself with the problem. Email the list if you don't understand the problem we are trying to solve. Also email the list the times you are available to meet (besides Friday discussions) so we can set up regular meetings. Nils |
|
From: Nils H. <nil...@uc...> - 2009-04-13 22:31:16
|
Professor Rupak, I am the contact for Project 7 and we have not been able to contact via email or in class (Friday or Monday) the following two project members. I looked up their email via the UCLA directory. Tasinga, Penn and Wong, Kenny They may have dropped the class, be sick, or some other reason. How should we proceed given we have only 5 reachable members? Finally, we met with the customers today and they mentioned instead of writing something from scratch, they wouldn't mind seeing a software that is composed of the best pieces of currently available tools, since they think this will get a more polished and advanced project by the end of the quarter. How do I respond to such a suggestion, or is it even acceptable, give our impression that we are to design and build everything from scratch? Sincerely, Nils ------ Forwarded Message > From: Nils Homer <nil...@uc...> > Date: Mon, 13 Apr 2009 10:04:03 -0700 > To: <pta...@uc...>, <nak...@ho...> > Conversation: CS 130 Project > Subject: CS 130 Project > > Hey Guys, > > You are assigned to Project 7. Please check the cs130 website for a > description of our project. We are going to meet with the customers after > class today (mon april 13). > > Please also set up a SF account, join the following project and its developers > mailing list asap. > https://sourceforge.net/projects/pipeline130/ > > Nils ------ End of Forwarded Message |
|
From: Chris S. <cs...@uc...> - 2009-04-13 03:26:36
|
At Nils' suggestion, I created a wiki page for the requirements presentation/document: https://apps.sourceforge.net/mediawiki/pipeline130/index.php?title=Requirements If you have any ideas, please just get them onto that page. Someone, please take notes during the client meeting tomorrow! -Chris |
|
From: Chris S. <cs...@uc...> - 2009-04-13 02:49:30
|
Didn't have access to the control panel ("special pages" -> user rights
management from within wiki), but it turns out there's a 'grant admin'
button from within SF (Project Admin -> Feature Settings) that worked.
For everyone's reference, you have to do that (and then log into wiki using
your SF info) before you can edit/make pages/etc.
--------------------------------------------------
From: "Nils Homer" <nil...@uc...>
Sent: Sunday, April 12, 2009 7:30 PM
To: "Chris Swan" <cs...@uc...>
Subject: Re: [Pipeline130-developers] DRMAA and Monday meeting
> Your an admin, do you not have the ability to access the wiki control
> panel?
>
>
> On 4/12/09 7:22 PM, "Chris Swan" <cs...@uc...> wrote:
>
>> You made us admins of the project, but the wiki still considers us
>> regular
>> users. I think you need to change it from within the wiki control panel.
>>
>> --------------------------------------------------
>> From: "Nils Homer" <nil...@uc...>
>> Sent: Sunday, April 12, 2009 3:33 PM
>> To: <cs...@uc...>
>> Subject: Re: [Pipeline130-developers] DRMAA and Monday meeting
>>
>>> I am going to make everyone admins, hopefully that will do it.
>>>
>>>
>>> On 4/12/09 3:01 PM, "cs...@uc..." <cs...@uc...> wrote:
>>>
>>>> I think you are the only one with permission to edit the wiki right
>>>> now. Can you add us to the "editor" group?
>>>>
>>>> Quoting Nils Homer <nil...@uc...>:
>>>>
>>>>> Could you start a new page on the wiki and then we can all help out
>>>>> getting
>>>>> this first assignment completed, along with the script for Wednesday.
>>>>>
>>>>> Nils
>>>>>
>>>>>
>>>>> On 4/12/09 2:43 PM, "cs...@uc..." <cs...@uc...> wrote:
>>>>>
>>>>>> I have class till 3 on Monday so I won't be able to make it to the
>>>>>> meeting, but I will try to stop by your lab. As punishment for not
>>>>>> going, I could present Wednesday, but I'll need help with the
>>>>>> script/powerpoint! Of course if anyone would rather do it I'd be
>>>>>> happy
>>>>>> to let them...
>>>>>>
>>>>>> DRMAA sounds like a good choice.
>>>>>>
>>>>>> -Chris
>>>>>>
>>>>>> Quoting Nils Homer <nil...@uc...>:
>>>>>>
>>>>>>>
>>>>>>> I am also scheduling a meeting for Monday right after class since
>>>>>>> the
>>>>>>> customers are not available before 12. If you can't make it to
>>>>>>> the meeting,
>>>>>>> you can stop by my Lab at 5554 Gonda before 5pm and we can catch up,
>>>>>>> or
>>>>>>> check the mailing lists and wiki for meeting notes.
>>>>>>>
>>>>>>> Are there any volunteers for Wednesday?
>>>>>>>
>>>>>>> Nils
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --------------------------------------------------------------------------
>>>>>> --
>>>>>> --
>>>>>> This SF.net email is sponsored by:
>>>>>> High Quality Requirements in a Collaborative Environment.
>>>>>> Download a free trial of Rational Requirements Composer Now!
>>>>>> http://p.sf.net/sfu/www-ibm-com
>>>>>> _______________________________________________
>>>>>> Pipeline130-developers mailing list
>>>>>> Pip...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/pipeline130-developers
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>>
>
>
>
|
6 messages has been excluded from this view by a project administrator.
