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Re: [Microbe] experiment service implemented and proposed specs
by Marcin Joachimiak 16 Jan '13

16 Jan '13

> > > Do you have a short spec in plain English? > > I'm not convinced that'd be helpful. The point of a typespec is that it > describes the API with related free text docs. > > Really I need comments from the people that are going to be > using/representing this data - e.g. Matt, Ben, Chris, Bill, Paramvir. I > suppose I shouldn't really send it out to the Microbes list as a whole, but > that's what I said I'd do in the meeting... eh. > Oh, but I do need to use and represent fitness and expression data within KBase which is why this service grabbed my attention. So the question is whether this is/will be the way to query and retrieve fitness data within KBase? I understand that you are targeting very specific things for the demo, but its a bit odd to tackle these without having any generic functionality in place. Based on the current structure I should expect a function in this spec a la 'returnFitnessDataForBiclustering' and 'returnExperimentDataForBiclustering'? Even 'returnTabData' or 'returnDataMatrix' would be fantastic. p.s. Looks like I sent an empty msg by accident moments ago, gmail can't undo those apparently.

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Re: [Microbe] experiment service implemented and proposed specs
by Marcin Joachimiak 16 Jan '13

16 Jan '13

On Wed, Jan 16, 2013 at 2:54 PM, Gavin A Price <gavinaprice(a)gmail.com>wrote: > From the service name a naive user would assume something generic for > experiment data and/or meta-data but this seems customized to FBA/KO strain > data and analysis? Shouldn't that be in a more specific service aka > 'FitnessDataforFBA' or 'FunctionalGenomicsDataForFBA'? > > It will be the former, up until the demo it's basically the latter. > > > What is 'maxKnockouts'? The number of replicate KO strains? > > The maximum knockouts a strain can possess if it is to be returned as part > of a dataset. > > > Do you have a short spec in plain English? > > I'm not convinced that'd be helpful. The point of a typespec is that it > describes the API with related free text docs. > > Really I need comments from the people that are going to be > using/representing this data - e.g. Matt, Ben, Chris, Bill, Paramvir. I > suppose I shouldn't really send it out to the Microbes list as a whole, but > that's what I said I'd do in the meeting... eh. > > -g > > > > On 1/16/2013 2:44 PM, Marcin Joachimiak wrote: > > Hi Gavin, > I take it you'll be happy with any comments at this point ... > > Do you have a short spec in plain English? > > From the service name a naive user would assume something generic for > experiment data and/or meta-data but this seems customized to FBA/KO strain > data and analysis? Shouldn't that be in a more specific service aka > 'FitnessDataforFBA' or 'FunctionalGenomicsDataForFBA'? > > What is 'maxKnockouts'? The number of replicate KO strains? > > Beyond that I can't comment since I don't know what this is supposed to > be for exactly. > > marcin > > > On Wed, Jan 16, 2013 at 2:06 PM, Gavin A Price <gavinaprice(a)gmail.com>wrote: > >> So is everyone ok with these specs? I'm working on something else on the >> moment so I'm not losing time, but I'm a bit surprised that no one has >> commented. >> >> -g >> >> >> On 1/14/2013 12:16 PM, Gavin A Price wrote: >> >>> I should point out that the methods you're going to want to look at are >>> generateGrowmatchInput and generateAndStoreGMInput. The others aren't >>> really controversial afaik. >>> >>> -g >>> >>> On 1/14/2013 12:14 PM, Gavin A Price wrote: >>> >>>> As discussed in the meeting this morning. >>>> >>>> -g >>>> >>> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/microbe >> > >

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Re: [Microbe] experiment service implemented and proposed specs
by Gavin A Price 16 Jan '13

16 Jan '13

> From the service name a naive user would assume something generic for > experiment data and/or meta-data but this seems customized to FBA/KO > strain data and analysis? Shouldn't that be in a more specific service > aka 'FitnessDataforFBA' or 'FunctionalGenomicsDataForFBA'? It will be the former, up until the demo it's basically the latter. > What is 'maxKnockouts'? The number of replicate KO strains? The maximum knockouts a strain can possess if it is to be returned as part of a dataset. > Do you have a short spec in plain English? I'm not convinced that'd be helpful. The point of a typespec is that it describes the API with related free text docs. Really I need comments from the people that are going to be using/representing this data - e.g. Matt, Ben, Chris, Bill, Paramvir. I suppose I shouldn't really send it out to the Microbes list as a whole, but that's what I said I'd do in the meeting... eh. -g On 1/16/2013 2:44 PM, Marcin Joachimiak wrote: > Hi Gavin, > I take it you'll be happy with any comments at this point ... > > Do you have a short spec in plain English? > > From the service name a naive user would assume something generic for > experiment data and/or meta-data but this seems customized to FBA/KO > strain data and analysis? Shouldn't that be in a more specific service > aka 'FitnessDataforFBA' or 'FunctionalGenomicsDataForFBA'? > > What is 'maxKnockouts'? The number of replicate KO strains? > > Beyond that I can't comment since I don't know what this is supposed > to be for exactly. > > marcin > > > On Wed, Jan 16, 2013 at 2:06 PM, Gavin A Price <gavinaprice(a)gmail.com > <mailto:[email protected]>> wrote: > > So is everyone ok with these specs? I'm working on something else > on the moment so I'm not losing time, but I'm a bit surprised that > no one has commented. > > -g > > > On 1/14/2013 12:16 PM, Gavin A Price wrote: > > I should point out that the methods you're going to want to > look at are generateGrowmatchInput and > generateAndStoreGMInput. The others aren't really > controversial afaik. > > -g > > On 1/14/2013 12:14 PM, Gavin A Price wrote: > > As discussed in the meeting this morning. > > -g > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us <mailto:[email protected]> > https://lists.kbase.us/mailman/listinfo/microbe > >

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Re: [Microbe] experiment service implemented and proposed specs
by Marcin Joachimiak 16 Jan '13

16 Jan '13

Hi Gavin, I take it you'll be happy with any comments at this point ... Do you have a short spec in plain English? >From the service name a naive user would assume something generic for experiment data and/or meta-data but this seems customized to FBA/KO strain data and analysis? Shouldn't that be in a more specific service aka 'FitnessDataforFBA' or 'FunctionalGenomicsDataForFBA'? What is 'maxKnockouts'? The number of replicate KO strains? Beyond that I can't comment since I don't know what this is supposed to be for exactly. marcin On Wed, Jan 16, 2013 at 2:06 PM, Gavin A Price <gavinaprice(a)gmail.com>wrote: > So is everyone ok with these specs? I'm working on something else on the > moment so I'm not losing time, but I'm a bit surprised that no one has > commented. > > -g > > > On 1/14/2013 12:16 PM, Gavin A Price wrote: > >> I should point out that the methods you're going to want to look at are >> generateGrowmatchInput and generateAndStoreGMInput. The others aren't >> really controversial afaik. >> >> -g >> >> On 1/14/2013 12:14 PM, Gavin A Price wrote: >> >>> As discussed in the meeting this morning. >>> >>> -g >>> >> ______________________________**_________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/**mailman/listinfo/microbe<https://lists.kbase.us/mailman/listinfo/microbe> >

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Re: [Microbe] experiment service implemented and proposed specs
by Gavin A Price 16 Jan '13

16 Jan '13

So is everyone ok with these specs? I'm working on something else on the moment so I'm not losing time, but I'm a bit surprised that no one has commented. -g On 1/14/2013 12:16 PM, Gavin A Price wrote: > I should point out that the methods you're going to want to look at > are generateGrowmatchInput and generateAndStoreGMInput. The others > aren't really controversial afaik. > > -g > > On 1/14/2013 12:14 PM, Gavin A Price wrote: >> As discussed in the meeting this morning. >> >> -g

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Re: [Microbe] experiment service implemented and proposed specs
by Gavin A Price 14 Jan '13

14 Jan '13

I should point out that the methods you're going to want to look at are generateGrowmatchInput and generateAndStoreGMInput. The others aren't really controversial afaik. -g On 1/14/2013 12:14 PM, Gavin A Price wrote: > As discussed in the meeting this morning. > > -g

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experiment service implemented and proposed specs
by Gavin A Price 14 Jan '13

14 Jan '13

As discussed in the meeting this morning. -g

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Re: [Microbe] No microbe meeting on Monday?
by Paramvir Dehal 14 Jan '13

14 Jan '13

1-866-740-1260 Code: 4958182# On Mon, Jan 14, 2013 at 11:00 AM, Matt DeJongh <dejongh(a)hope.edu> wrote: > Please send around the number/passcode. > > Matt > > > On Sun, Jan 13, 2013 at 11:22 PM, Psdehal <psdehal(a)lbl.gov> wrote: > >> Yeah, we've got a meeting. 11am pacific. I'll get it back on the calendar. >> >> Sent from my iPad >> >> On Jan 12, 2013, at 10:32 AM, Gavin A Price <gavinaprice(a)gmail.com> >> wrote: >> >> > There's no microbes meeting on the KBase calendar for Monday. I assume >> that's wrong and we are having a meeting? >> > >> > -g >> > _______________________________________________ >> > Microbe mailing list >> > Microbe(a)lists.kbase.us >> > https://lists.kbase.us/mailman/listinfo/microbe >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/microbe >> > > > > -- > Matt DeJongh, Ph.D. > Computer Science Department > Hope College, Holland, MI 49423 > (616) 395-7429 >

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Re: [Microbe] No microbe meeting on Monday?
by Matt DeJongh 14 Jan '13

14 Jan '13

Please send around the number/passcode. Matt On Sun, Jan 13, 2013 at 11:22 PM, Psdehal <psdehal(a)lbl.gov> wrote: > Yeah, we've got a meeting. 11am pacific. I'll get it back on the calendar. > > Sent from my iPad > > On Jan 12, 2013, at 10:32 AM, Gavin A Price <gavinaprice(a)gmail.com> wrote: > > > There's no microbes meeting on the KBase calendar for Monday. I assume > that's wrong and we are having a meeting? > > > > -g > > _______________________________________________ > > Microbe mailing list > > Microbe(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/microbe > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > -- Matt DeJongh, Ph.D. Computer Science Department Hope College, Holland, MI 49423 (616) 395-7429

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Re: [Microbe] No microbe meeting on Monday?
by Psdehal 13 Jan '13

13 Jan '13

Yeah, we've got a meeting. 11am pacific. I'll get it back on the calendar. Sent from my iPad On Jan 12, 2013, at 10:32 AM, Gavin A Price <gavinaprice(a)gmail.com> wrote: > There's no microbes meeting on the KBase calendar for Monday. I assume that's wrong and we are having a meeting? > > -g > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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