April 2013 - Microbe - mailman3.cels.anl.gov

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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