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Re: [Microbe] campaigns for Adam
by Marcin Joachimiak 11 Apr '13

11 Apr '13

Hey Paramvir, One higher level theme is regulation. At the moment it looks like the plant and microbe regulatory network efforts will take parallel paths. But there are some common threads, at the very least the plant and microbe regulation could be cast into a common data model. The elements of the regulatory network are also common (regulator, target, type of interaction), though things like network and regulon size may be operationally different. Biclusters are operationally the same (again with size and overlap differences). Motifs may be qualitatively different. So there are some nuances, but fundamentally it seems that the methods to reconstruct the networks can be common. Also the 'plant-microbes' interaction theme suggests that at some point we may consider combined regulatory models. There are also higher level themes in annotation. Currently the Networks team is starting to explore network based annotation and this will have both a plants and microbe direction. Same for functional ortholog prediction. Just wanted to throw this out there for consideration ... marcin On Thu, Apr 11, 2013 at 10:47 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > So it looks like we're making pretty good head way on our 3 month Platform > campaigns doc. Chris and I will prioritize them before we send them to Adam > and Rick. > > > https://docs.google.com/a/lbl.gov/document/d/1Nz2Tjl6Vdj9XWnEWEVHjWkJRew0jE… > > > Also take a look at our science campaigns, we don't have these broken down > into sprints, but I think it's okay to keep them at an intermediate level: > > > https://docs.google.com/a/lbl.gov/document/d/1AsdNq-umcYFBnijFSm3RzBXtKW-M9… > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > >

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campaigns for Adam
by Paramvir Dehal 11 Apr '13

11 Apr '13

So it looks like we're making pretty good head way on our 3 month Platform campaigns doc. Chris and I will prioritize them before we send them to Adam and Rick. https://docs.google.com/a/lbl.gov/document/d/1Nz2Tjl6Vdj9XWnEWEVHjWkJRew0jE… Also take a look at our science campaigns, we don't have these broken down into sprints, but I think it's okay to keep them at an intermediate level: https://docs.google.com/a/lbl.gov/document/d/1AsdNq-umcYFBnijFSm3RzBXtKW-M9…

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Re: [Microbe] reminder! update the google doc
by Gavin Price 10 Apr '13

10 Apr '13

We should just get a sysbiokbase tag going on SO. -g On 4/10/2013 1:02 PM, Ben Bowen wrote: > Thanks Terry! That is exactly what I wanted, and it ran perfectly in > IRIS! I'll work on wrapping my mind around how to teach people how to > create queries like that themselves. The simplest thing that comes to > mind is something like StackOverflow where people post little > questions (like mine) and experts put in how to do it correctly. > > Ben > > -------------- > Email: BPBowen(a)lbl.gov <mailto:[email protected]> > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov <http://ms.lbl.gov> > > > On Wed, Apr 10, 2013 at 12:47 PM, Terry Disz <disz(a)mcs.anl.gov > <mailto:[email protected]>> wrote: > > Ben, > > Ross and I took this up and we produced this example - I think it > does what you want. > We went to the ERDB browser and followed the path from > Compound->ParticipatesAs->LocalizedCompund->IsInvolvedIn > > > > all_entities_Compound -a | grep -i valine | > get_relationship_ParticipatesAs -c 1 -to id | > get_relationship_IsInvolvedIn -to id,name > > This produces information for all compounds with valine in the name. > > Here are the first couple lines of output > > disz@ash:~$ all_entities_Compound -a | grep -i valine | > get_relationship_ParticipatesAs -c 1 -to id | > get_relationship_IsInvolvedIn -to id,name > kb|cpd.153L-Valineval-Lcpd0015601340988351117C5H11NO20-86.490.43806kb|loc.0.c.1376kb|rxn.99L-valine > transport in via proton symport > kb|cpd.153L-Valineval-Lcpd0015601340988351117C5H11NO20-86.490.43806kb|loc.0.c.1376kb|rxn.485Branched > chain amino acid:H+ symporter (Valine) > > Is this what you were looking for? > > Terry > > > > On Apr 10, 2013, at 2:17 PM, Ben Bowen <ben.bowen(a)gmail.com > <mailto:[email protected]>> wrote: > >> I just made a small update to the doc, but probably didn't make >> it clear. The thought I'm trying to convey is that we are >> missing out on a huge opportunity by not having the API commands >> that perform ER-queries easier to use. To me, the ER-queries >> make the KBase platform very distinct (and more powerful) from >> other systems. I just can never seem to get them to work... >> maybe its just me, but somehow I doubt it. Today, I was trying >> to get a list of reactions that Valine was involved in and I gave >> up after 30 minutes. Actually, what I was trying to do was this: >> 1) get all the relationships that connect "Compounds" >> 2) for Valine, get all the results of those relationships (ie: >> Media IDs, Biomass terms, Reactions, etc). >> What a powerful query! and what a success it would be to somehow >> make it easier. I don't know what this would take, but I'm happy >> to talk with whoever wants to try and figure out what it would take. >> >> Ben >> >> >> -------------- >> Email: BPBowen(a)lbl.gov <mailto:[email protected]> >> Phone: (510) 214-6683 <tel:%28510%29%20214-6683> >> MS 977-221, Lawrence Berkeley Lab >> Web: ms.lbl.gov <http://ms.lbl.gov/> >> >> >> On Tue, Apr 9, 2013 at 12:18 PM, Paramvir Dehal <psdehal(a)lbl.gov >> <mailto:[email protected]>> wrote: >> >> Adam want's our Platform updates by Thursday, please update >> the google doc: >> >> https://docs.google.com/a/lbl.gov/document/d/1Nz2Tjl6Vdj9XWnEWEVHjWkJRew0jE… >> >> Let's populate this as much as we can before trying to >> prioritize. >> >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us <mailto:[email protected]> >> https://lists.kbase.us/mailman/listinfo/microbe >> >> >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us <mailto:[email protected]> >> https://lists.kbase.us/mailman/listinfo/microbe > > > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] reminder! update the google doc
by Ben Bowen 10 Apr '13

10 Apr '13

Thanks Terry! That is exactly what I wanted, and it ran perfectly in IRIS! I'll work on wrapping my mind around how to teach people how to create queries like that themselves. The simplest thing that comes to mind is something like StackOverflow where people post little questions (like mine) and experts put in how to do it correctly. Ben -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Wed, Apr 10, 2013 at 12:47 PM, Terry Disz <disz(a)mcs.anl.gov> wrote: > Ben, > > Ross and I took this up and we produced this example - I think it does > what you want. > We went to the ERDB browser and followed the path from > Compound->ParticipatesAs->LocalizedCompund->IsInvolvedIn > > > > all_entities_Compound -a | grep -i valine | > get_relationship_ParticipatesAs -c 1 -to id | get_relationship_IsInvolvedIn > -to id,name > > This produces information for all compounds with valine in the name. > > Here are the first couple lines of output > > disz@ash:~$ all_entities_Compound -a | grep -i valine | > get_relationship_ParticipatesAs -c 1 -to id | get_relationship_IsInvolvedIn > -to id,name > kb|cpd.153 L-Valine val-L cpd00156 0 1340988351 117 C5H11NO2 0 -86.49 > 0.43806 kb|loc.0.c.1376 kb|rxn.99 L-valine transport in via proton symport > kb|cpd.153 L-Valine val-L cpd00156 0 1340988351 117 C5H11NO2 0 -86.49 > 0.43806 kb|loc.0.c.1376 kb|rxn.485 Branched chain amino acid:H+ symporter > (Valine) > > Is this what you were looking for? > > Terry > > > > On Apr 10, 2013, at 2:17 PM, Ben Bowen <ben.bowen(a)gmail.com> wrote: > > I just made a small update to the doc, but probably didn't make it clear. > The thought I'm trying to convey is that we are missing out on a huge > opportunity by not having the API commands that perform ER-queries easier > to use. To me, the ER-queries make the KBase platform very distinct (and > more powerful) from other systems. I just can never seem to get them to > work... maybe its just me, but somehow I doubt it. Today, I was trying to > get a list of reactions that Valine was involved in and I gave up after 30 > minutes. Actually, what I was trying to do was this: > 1) get all the relationships that connect "Compounds" > 2) for Valine, get all the results of those relationships (ie: Media IDs, > Biomass terms, Reactions, etc). > What a powerful query! and what a success it would be to somehow make it > easier. I don't know what this would take, but I'm happy to talk with > whoever wants to try and figure out what it would take. > > Ben > > > -------------- > Email: BPBowen(a)lbl.gov > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov > > > On Tue, Apr 9, 2013 at 12:18 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > >> Adam want's our Platform updates by Thursday, please update the google >> doc: >> >> >> https://docs.google.com/a/lbl.gov/document/d/1Nz2Tjl6Vdj9XWnEWEVHjWkJRew0jE… >> >> Let's populate this as much as we can before trying to prioritize. >> >> _______________________________________________ >> 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 > > >

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Re: [Microbe] reminder! update the google doc
by Terry Disz 10 Apr '13

10 Apr '13

Ben, Ross and I took this up and we produced this example - I think it does what you want. We went to the ERDB browser and followed the path from Compound->ParticipatesAs->LocalizedCompund->IsInvolvedIn all_entities_Compound -a | grep -i valine | get_relationship_ParticipatesAs -c 1 -to id | get_relationship_IsInvolvedIn -to id,name This produces information for all compounds with valine in the name. Here are the first couple lines of output disz@ash:~$ all_entities_Compound -a | grep -i valine | get_relationship_ParticipatesAs -c 1 -to id | get_relationship_IsInvolvedIn -to id,name kb|cpd.153 L-Valine val-L cpd00156 0 1340988351 117 C5H11NO2 0 -86.49 0.43806 kb|loc.0.c.1376 kb|rxn.99 L-valine transport in via proton symport kb|cpd.153 L-Valine val-L cpd00156 0 1340988351 117 C5H11NO2 0 -86.49 0.43806 kb|loc.0.c.1376 kb|rxn.485 Branched chain amino acid:H+ symporter (Valine) Is this what you were looking for? Terry On Apr 10, 2013, at 2:17 PM, Ben Bowen <ben.bowen(a)gmail.com> wrote: > I just made a small update to the doc, but probably didn't make it clear. The thought I'm trying to convey is that we are missing out on a huge opportunity by not having the API commands that perform ER-queries easier to use. To me, the ER-queries make the KBase platform very distinct (and more powerful) from other systems. I just can never seem to get them to work... maybe its just me, but somehow I doubt it. Today, I was trying to get a list of reactions that Valine was involved in and I gave up after 30 minutes. Actually, what I was trying to do was this: > 1) get all the relationships that connect "Compounds" > 2) for Valine, get all the results of those relationships (ie: Media IDs, Biomass terms, Reactions, etc). > What a powerful query! and what a success it would be to somehow make it easier. I don't know what this would take, but I'm happy to talk with whoever wants to try and figure out what it would take. > > Ben > > > -------------- > Email: BPBowen(a)lbl.gov > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov > > > On Tue, Apr 9, 2013 at 12:18 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Adam want's our Platform updates by Thursday, please update the google doc: > > https://docs.google.com/a/lbl.gov/document/d/1Nz2Tjl6Vdj9XWnEWEVHjWkJRew0jE… > > Let's populate this as much as we can before trying to prioritize. > > _______________________________________________ > 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

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Re: [Microbe] reminder! update the google doc
by Ben Bowen 10 Apr '13

10 Apr '13

I just made a small update to the doc, but probably didn't make it clear. The thought I'm trying to convey is that we are missing out on a huge opportunity by not having the API commands that perform ER-queries easier to use. To me, the ER-queries make the KBase platform very distinct (and more powerful) from other systems. I just can never seem to get them to work... maybe its just me, but somehow I doubt it. Today, I was trying to get a list of reactions that Valine was involved in and I gave up after 30 minutes. Actually, what I was trying to do was this: 1) get all the relationships that connect "Compounds" 2) for Valine, get all the results of those relationships (ie: Media IDs, Biomass terms, Reactions, etc). What a powerful query! and what a success it would be to somehow make it easier. I don't know what this would take, but I'm happy to talk with whoever wants to try and figure out what it would take. Ben -------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Tue, Apr 9, 2013 at 12:18 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Adam want's our Platform updates by Thursday, please update the google doc: > > > https://docs.google.com/a/lbl.gov/document/d/1Nz2Tjl6Vdj9XWnEWEVHjWkJRew0jE… > > Let's populate this as much as we can before trying to prioritize. > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > >

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reminder! update the google doc
by Paramvir Dehal 09 Apr '13

09 Apr '13

Adam want's our Platform updates by Thursday, please update the google doc: https://docs.google.com/a/lbl.gov/document/d/1Nz2Tjl6Vdj9XWnEWEVHjWkJRew0jE… Let's populate this as much as we can before trying to prioritize.

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Re: [Microbe] Microbes Call
by Paramvir Dehal 08 Apr '13

08 Apr '13

Here's the google doc for our 3 month Platform Goals: https://docs.google.com/a/lbl.gov/document/d/1Nz2Tjl6Vdj9XWnEWEVHjWkJRew0jE… I added some items that came up before, but you shouldn't take them too seriously. I also need to add the things we came up with during the all hands meeting. At this point, let's fill out the list and we'll prioritize afterwards. Paramvir On Mon, Apr 8, 2013 at 9:58 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Call today at 11am P / 1pm C > > *866-740-1260 Code: 4958182 * > > The call should be brief. We'll talk about last weeks all hands meeting > and what it means for us. I'd like to focus on enumerating and prioritizing > the campaigns for the first 3 month where we shore up our platform. I'll > start a google doc and send it out before the call. > > Paramvir >

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Microbes Call
by Paramvir Dehal 08 Apr '13

08 Apr '13

Call today at 11am P / 1pm C *866-740-1260 Code: 4958182 * The call should be brief. We'll talk about last weeks all hands meeting and what it means for us. I'd like to focus on enumerating and prioritizing the campaigns for the first 3 month where we shore up our platform. I'll start a google doc and send it out before the call. Paramvir

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Finalizing All hands meeting agenda
by Christopher Henry 25 Mar '13

25 Mar '13

Hi Nomi, Many people, like me, won't be able to attend the all hands meeting in person. Will there be a dial in number for the meeting (video would be even better) so we can participate remotely? If so, can we figure that out and distribute information on it soon so our people can plan? Also, I sent out the tentative agenda from this mornings meeting to our team. Do we know when a finalized agenda will be available? Chris

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