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

Demo success
by Christopher Henry 27 Feb '13

27 Feb '13

Dear microbes team, I wanted to give a quick update about how the demo went. I know the microbes demo was well attended, and the audience seemed to be very interested in what we had to present. After the demo, many folks approached us with the goal of getting their methods and data in KBase. My understanding is all the demos went very well, and the DOE program managers were thrilled with the results. The demo talks with our scientific collaborators also went very well. So overall, I would call the GTL meeting a resounding success for KBase. Paramvir and I would like to extend our deep thanks to all of you for your hard work in getting this project to this very successful intermediate stage. This is just the beginning, but it's a critical beginning because I think we have decisively proved our worth to the community. Nice work everyone. Let's keep it going! Chris

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KBase Metabolic Modeling Bootcamp: Friday Noon-2PM central time
by Christopher Henry 21 Feb '13

21 Feb '13

Hello everyone, We will be holding a KBase Modeling Bootcamp tomorrow (Friday) from Noon-2PM central time. As we have done previously, we will hold the bootcamp on webex. The meeting connection information is: Where: https://meetings.webex.com/ Meeting number: 195 363 936 Password: This meeting does not require a password. Also, as previously, I would like to offer a conference call number for people to use for audio. The conference call number will be: US/CAN Toll Free: 1-888-850-4523 Participant Passcode: 913601 Don't use the webex number. Please be aware, I am RECORDING these bootcamps (audio and screen cast) for posting online. In this boot camp, we will use IRIS: http://prototypesite.net/iris/ We will use the workspace browser: http://140.221.92.49/ We will probably explore a number of KBase labs: http://www.kbase.us/labs/ And I'll be using this google doc to store commands to make it easier to follow along: https://docs.google.com/document/d/1zwlrCMpMqGWjigjxFwihzcpsx_F69Uk8s9FxWtm… So load up your phenotype data… warm up your Globus KBase account… pick out your favorite genome, and get ready to have some modeling fun!!! And bring a notebook and sharpened pencils… because I definitely want feedback. Sorry for the late notice. If you can't make it to this one, not to fear. There will be many many more. Also, we post videos online: http://205.208.105.217/KBaseBootCamp01.html I'm going to go ahead and officially schedule the FIRST post demo Modeling Bootcamp: Friday, March 15, 1-3 PM central time Best regards, Chris

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Fwd: KBase Metabolic Modeling Bootcamp: Friday 1-3PM central time
by Christopher Henry 20 Feb '13

20 Feb '13

Hi all, New link for the bootcamp video: http://205.208.105.217/KBaseBootCamp01.html The previous link pointed to a truncated video. Chris Begin forwarded message: > From: Dr Ric Colasanti <ric.colasanti(a)gmail.com> > Subject: Re: KBase Metabolic Modeling Bootcamp: Friday 1-3PM central time > Date: February 20, 2013 8:09:00 PM CST > To: Christopher Henry <chrisshenry(a)gmail.com> > Cc: Matt DeJongh <dejongh(a)hope.edu>, Aaron Best <best(a)hope.edu>, Jonathan Ko <jonathan.ko(a)gmail.com>, Pamela Weisenhorn <weise088(a)umn.edu>, José Faria Pedro Lopes <jplfaria(a)gmail.com>, Paul Frybarger <pfrybarger(a)gmail.com>, Sam Seaver <samseaver(a)gmail.com>, "janaka.e(a)gmail.com Edirisinghe" <janaka.e(a)gmail.com>, Ross Overbeek <rossoverbeek(a)gmail.com>, Ronald Taylor <ronald.taylor24(a)gmail.com>, Becky M Hess <Becky.Hess(a)pnnl.gov>, Ben Bowen <bpbowen(a)lbl.gov>, Neal Conrad <nconrad(a)mcs.anl.gov>, Soh Keng Cher <kengcher.soh(a)epfl.ch>, "Michael B. (Mike) Mundy" <Mundy.Michael(a)mayo.edu>, Matthew Benedict <matthew.n.benedict(a)gmail.com>, RaphyZ zarecki <raphy.zarecki(a)gmail.com>, Tammy Khazaei <tkhazaei(a)caltech.edu>, Rebecca Wattam <wattam(a)vbi.vt.edu>, "Elizabeth M. Glass" <marland(a)mcs.anl.gov>, J Fessler Salazar <jsalazar(a)anl.gov> > > http://205.208.105.217/KBaseBootCamp01.html Complete boot camp is now available > All the best > Ric > > > On 20 February 2013 18:42, Dr Ric Colasanti <ric.colasanti(a)gmail.com> wrote: > http://205.208.105.217/KBaseBootCamp01.html First installment At the moment works best with Chrome > > Ric > > > On 20 February 2013 18:07, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Bootcamp video is simple streaming form: > http://205.208.105.217/VideoTest.html > Many thanks to Ric for setting this up. > BTW, make it full screen… otherwise it won't look good. > > On Feb 14, 2013, at 1:51 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > > > Hello everyone, > > > > We will be holding a KBase Modeling Bootcamp tomorrow (Friday) from 1-3PM central time. As we have done previously, we will hold the bootcamp on webex. The meeting connection information is: > > Where: https://meetings.webex.com/ > > Meeting number: 196 404 043 > > Password: This meeting does not require a password. > > > > Also, as previously, I would like to offer a conference call number for people to use for audio. The conference call number will be: > > US/CAN Toll Free: 1-888-850-4523 > > Participant Passcode: 913601 > > > > Don't use the webex number. Please be aware, I am RECORDING these bootcamps (audio and screen cast) for posting online. > > > > In this boot camp, we will use IRIS: > > http://140.221.84.183/iris/Iris/# > > > > And we will use the new improved workspace browser: > > http://140.221.92.49/new/ > > > > So load up your phenotype data… warm up your Globus KBase account… pick out your favorite genome, and get ready to have some modeling fun!!! > > And bring a notebook and sharpened pencils… because I definitely want feedback. > > > > Sorry for the late notice. If you can't make it to this one, not to fear. There will be many many more. > > > > Best regards, > > > > Chris > > > > >

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Re: [Microbe] KBase Metabolic Modeling Bootcamp: Friday 1-3PM central time
by Christopher Henry 20 Feb '13

20 Feb '13

The bootcamp video is posted in simple streaming form: http://205.208.105.217/VideoTest.html Many thanks to Ric for setting this up. BTW, make it full screen… otherwise it won't look good. On Feb 14, 2013, at 1:44 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > Hello everyone, > > We will be holding a KBase Modeling Bootcamp tomorrow (Friday) from 1-3PM central time. As we have done previously, we will hold the bootcamp on webex. The meeting connection information is below. > > Also, as previously, I would like to offer a conference call number for people to use for audio. The conference call number will be: > US/CAN Toll Free: 1-888-850-4523 > Participant Passcode: 913601 > > Don't use the webex number. Please be aware, I am RECORDING these bootcamps (audio and screen cast) for posting online. > > In this boot camp, we will use IRIS: > http://140.221.84.183/iris/Iris/# > > And we will use the new improved workspace browser: > http://140.221.92.49/new/ > > So load up your phenotype data… warm up your Globus KBase account… pick out your favorite genome, and get ready to have some modeling fun!!! > And bring a notebook and sharpened pencils… because I definitely want feedback. > > Sorry for the late notice. If you can't make it to this one, not to fear. There will be many many more. > > Best regards, > > Chris > >> >> Hi, >> >> >> Christopher Henry is inviting you to this WebEx meeting: >> >> KBase Metabollic Modeling Bootcamp >> Fri, Feb 15, 1:00 pm | 2 hr >> Chicago (Central Standard Time, GMT-06:00) >> Host: Christopher Henry >> >> Join >> >> >> Add the attached iCalendar (.ics) file to your calendar. >> >> Agenda >> >> This meeting does not have an agenda. >> >> Access Information >> >> Where: WebEx Online >> Meeting number: 196 404 043 >> Password: This meeting does not require a password. >> >> Audio Connection >> >> 1-650-479-3207 US TOLL >> Access code: 196 404 043 >> >> Meeting Files (0) >> >> Can't access your meeting? Get help. >> Delivering the power of collaboration, >> Cisco WebEx Team >> >> IMPORTANT NOTICE: This WebEx service includes a feature that allows audio and any documents and other materials exchanged or viewed during the meeting to be recorded. By joining this meeting, you automatically consent to such recordings. If you do not consent to the recording, discuss your concerns with the meeting host prior to the start of the recording or do not join the meeting. Please note that any such recordings may be subject to discovery in the event of litigation. >> >> ©2012 Cisco and/or its affiliates. All rights reserved. >> MT-A-001 >> > <KBase Metabollic Modeling Bootcamp.ics> >

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Re: [Microbe] is there a conference call today?
by Christopher Henry 18 Feb '13

18 Feb '13

I believe we decided to have the meeting tomorrow at 1PM central. Chris On Feb 18, 2013, at 1:01 PM, Matt DeJongh <dejongh(a)hope.edu> wrote: > > > -- > Matt DeJongh, Ph.D. > Computer Science Department > Hope College, Holland, MI 49423 > (616) 395-7429 > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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is there a conference call today?
by Matt DeJongh 18 Feb '13

18 Feb '13

-- Matt DeJongh, Ph.D. Computer Science Department Hope College, Holland, MI 49423 (616) 395-7429

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Re: [Microbe] Demo data
by Paramvir Dehal 14 Feb '13

14 Feb '13

Hey Chris, small set back. I used: root@psd-v20:~/blast# cat kb.prok.genome.lst | genomes_to_fids | fids_to_protein_sequences > kb.proteome.fa and ran out of disk space after 5hrs. I'll restart and try and have it finished tonight. Paramvir On Thu, Feb 14, 2013 at 11:37 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Hey Chris, > > I'll take care of the BLAST'ing > > Paramvir > > > On Thu, Feb 14, 2013 at 9:37 AM, Christopher Henry <chrisshenry(a)gmail.com>wrote: > >> Hi all, >> >> So I have a couple of really URGENT requests for data and help I need >> with the Adam D. demo. >> >> 1.) I need a list of ALL paralogs in the g.20848 genome (related to >> mutant phenotype analysis) >> -Please blast all g.20848 genes against the g.20848 genome and >> provide me with a list of all hits >> -The list should have two columns: gene ID and blast score (and >> other blast metrics) >> >> 2.) I need a list of ALL hits between genes in the g.20848 genome and >> genomes in KBase (related to mutant phenotype analysis) >> -Provide me with a four column list: gene ID in g.20848, gene ID >> of hit in other genome, annotation of gene we hit, blast score, maybe other >> blast metrics >> >> 3.) MOST URGENT: I had issues with the wild type conditions Ben sent >> (related to IMMEDIATE phenotype analysis) >> -you gave me 100 conditions, but there were many repeated >> conditions (any idea why???) >> -You gave me some conditions that had no phosphate source at all >> >> I translated your wild type conditions into 60 media formulations (listed >> below). In the list below, the name of the media is in the first column, >> and the full list of compounds is in the second column. The prefix in the >> media name reflects my understanding of the study: >> "C-" means a study of carbon source >> "N-" means a study of nitrogen source >> "CN-" means a single compound serving as carbon and nitrogen source >> "P-" means phosphate source >> "S-" means sulfate source >> >> Note, I actually had to change three of your conditions because there was >> no phosphate source at all. But now I'm uncertain how these correspond to >> your knockout phenotypes. Can you resend me the knockout phenotype data >> specified in terms of my media names below? And can you send it today >> (ASAP)? If I have it by tonight, everything will be done tomorrow. >> >> Chris >> >> P.S. I understand (well… really really hope!) there are services in KBase >> to get me (1) and (2), and I'd love to hear about them. HOWEVER, please >> also run the commands yourself and send me the requested data directly… I >> need to try and shave time wherever possible. >> >> P.P.S. All work is being conducted in workspace "phenotypeDemo" >> >> C-Butyrate >> Butyrate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-Cytidine >> Cytidine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-Lactate >> D-Lactate;L-Lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-D-Lactate >> D-Lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-Guanosine >> Guanosine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-Inosine >> Inosine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-glutamate L-glutamic >> acid;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-glutamine >> L-glutamine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-isoleucine >> L-isoleucine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-lactate >> L-lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-leucine >> L-leucine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-serine >> L-serine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-N-acetyl-D-glucosamine >> N-acetyl-D-glucosamine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-acetate >> NH4+;Phosphate;Sulfate;acetate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-adenosine >> NH4+;Phosphate;Sulfate;adenosine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-alpha-ketoglutarate NH4+;Phosphate;Sulfate;alpha ketoglutaric >> acid;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-gly-asp-L >> NH4+;Phosphate;Sulfate;gly-asp-L;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-gly-glu-L >> NH4+;Phosphate;Sulfate;gly-glu-L;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-malate NH4+;Phosphate;Sulfate;malic >> acid;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-propionate >> NH4+;Phosphate;Sulfate;propionate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-pyruvate >> NH4+;Phosphate;Sulfate;pyruvate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-Uridine >> NH4+;Phosphate;Sulfate;Uridine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-Cytidine >> Cytidine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-glutamate L-glutamic >> acid;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-glutamine >> L-glutamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-isoleucine >> L-isoleucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-serine >> L-serine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-threonine >> L-threonine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-Aspartate Aspartic >> acid;D-Lactate;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-Arginine >> D-Lactate;L-Arginine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-Asparagine >> D-Lactate;L-Asparagine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-Glycine >> D-Lactate;L-Glycine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-Histidine >> D-Lactate;L-Histidine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-alanine >> D-Lactate;L-Lactate;L-alanine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-asparagine >> D-Lactate;L-Lactate;L-asparagine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-glutamate D-Lactate;L-Lactate;L-glutamic >> acid;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-glutamine >> D-Lactate;L-Lactate;L-glutamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-glycine >> D-Lactate;L-Lactate;L-glycine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-isoleucine >> D-Lactate;L-Lactate;L-isoleucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-leucine >> D-Lactate;L-Lactate;L-leucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-methionine >> D-Lactate;L-Lactate;L-methionine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-phenylalanine >> D-Lactate;L-Lactate;L-phenylalanine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-proline >> D-Lactate;L-Lactate;L-proline;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-serine >> D-Lactate;L-Lactate;L-serine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-threonine >> D-Lactate;L-Lactate;L-threonine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-N-acetyl-D-glucosamine >> D-Lactate;L-Lactate;N-acetyl-D-glucosamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-Adenosine >> D-Lactate;L-Lactate;Phosphate;Sulfate;adenosine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-Putrescine >> D-Lactate;L-Lactate;Phosphate;Sulfate;putrescine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-N-acetyl-D-glucosamine >> N-acetyl-D-glucosamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> P-Cytidine-5-monophosphate D-Lactate;L-Lactate;NH4+;Sulfate;cytidine >> 5' >> monophosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> P-Glycerol-3-phosphate D-Lactate;L-Lactate;NH4+;Sulfate;glycerol >> 3-phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> P-O-phosphoryl-ethanolamine >> D-Lactate;L-Lactate;NH4+;Sulfate;o-phosphoryl-ethanolamine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> P-Tripolyphosphate >> D-Lactate;L-Lactate;NH4+;Sulfate;tripolyphosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Cysteine >> Cysteine;D-Lactate;L-Lactate;NH4+;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Glutathione >> D-Lactate;L-Lactate;NH4+;glutathione;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Hypotaurine >> D-Lactate;L-Lactate;NH4+;hypotaurine;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Sulfate >> D-Lactate;L-Lactate;NH4+;Sulfate;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Sulfite >> D-Lactate;L-Lactate;NH4+;sulfite;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Thiosulfate >> D-Lactate;L-Lactate;NH4+;thiosulfate;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Thiourea >> D-Lactate;L-Lactate;NH4+;thiourea;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > > >

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Re: [Microbe] Demo data
by Ben Bowen 14 Feb '13

14 Feb '13

Hi Chris, Attached is the KO data, base media and WT data (without CAS amino acids, with no replicates, and with Phosphate added to the missing media definitions). You are also correct that there are many replicates in there. I thought we wanted to keep them in there to compare the KO results more easily. I took them out. Ben ----------------------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov On Thu, Feb 14, 2013 at 11:37 AM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Hey Chris, > > I'll take care of the BLAST'ing > > Paramvir > > > On Thu, Feb 14, 2013 at 9:37 AM, Christopher Henry <chrisshenry(a)gmail.com> > wrote: >> >> Hi all, >> >> So I have a couple of really URGENT requests for data and help I need with >> the Adam D. demo. >> >> 1.) I need a list of ALL paralogs in the g.20848 genome (related to mutant >> phenotype analysis) >> -Please blast all g.20848 genes against the g.20848 genome and >> provide me with a list of all hits >> -The list should have two columns: gene ID and blast score (and >> other blast metrics) >> >> 2.) I need a list of ALL hits between genes in the g.20848 genome and >> genomes in KBase (related to mutant phenotype analysis) >> -Provide me with a four column list: gene ID in g.20848, gene ID >> of hit in other genome, annotation of gene we hit, blast score, maybe other >> blast metrics >> >> 3.) MOST URGENT: I had issues with the wild type conditions Ben sent >> (related to IMMEDIATE phenotype analysis) >> -you gave me 100 conditions, but there were many repeated >> conditions (any idea why???) >> -You gave me some conditions that had no phosphate source at all >> >> I translated your wild type conditions into 60 media formulations (listed >> below). In the list below, the name of the media is in the first column, and >> the full list of compounds is in the second column. The prefix in the media >> name reflects my understanding of the study: >> "C-" means a study of carbon source >> "N-" means a study of nitrogen source >> "CN-" means a single compound serving as carbon and nitrogen source >> "P-" means phosphate source >> "S-" means sulfate source >> >> Note, I actually had to change three of your conditions because there was >> no phosphate source at all. But now I'm uncertain how these correspond to >> your knockout phenotypes. Can you resend me the knockout phenotype data >> specified in terms of my media names below? And can you send it today >> (ASAP)? If I have it by tonight, everything will be done tomorrow. >> >> Chris >> >> P.S. I understand (well… really really hope!) there are services in KBase >> to get me (1) and (2), and I'd love to hear about them. HOWEVER, please also >> run the commands yourself and send me the requested data directly… I need to >> try and shave time wherever possible. >> >> P.P.S. All work is being conducted in workspace "phenotypeDemo" >> >> C-Butyrate >> Butyrate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-Cytidine >> Cytidine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-Lactate >> D-Lactate;L-Lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-D-Lactate >> D-Lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-Guanosine >> Guanosine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-Inosine >> Inosine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-glutamate L-glutamic >> acid;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-glutamine >> L-glutamine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-isoleucine >> L-isoleucine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-lactate >> L-lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-leucine >> L-leucine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-L-serine >> L-serine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-N-acetyl-D-glucosamine >> N-acetyl-D-glucosamine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-acetate >> NH4+;Phosphate;Sulfate;acetate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-adenosine >> NH4+;Phosphate;Sulfate;adenosine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-alpha-ketoglutarate NH4+;Phosphate;Sulfate;alpha ketoglutaric >> acid;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-gly-asp-L >> NH4+;Phosphate;Sulfate;gly-asp-L;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-gly-glu-L >> NH4+;Phosphate;Sulfate;gly-glu-L;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-malate NH4+;Phosphate;Sulfate;malic >> acid;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-propionate >> NH4+;Phosphate;Sulfate;propionate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-pyruvate >> NH4+;Phosphate;Sulfate;pyruvate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> C-Uridine >> NH4+;Phosphate;Sulfate;Uridine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-Cytidine >> Cytidine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-glutamate L-glutamic >> acid;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-glutamine >> L-glutamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-isoleucine >> L-isoleucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-serine >> L-serine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-threonine >> L-threonine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-Aspartate Aspartic >> acid;D-Lactate;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-Arginine >> D-Lactate;L-Arginine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-Asparagine >> D-Lactate;L-Asparagine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-Glycine >> D-Lactate;L-Glycine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-Histidine >> D-Lactate;L-Histidine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-alanine >> D-Lactate;L-Lactate;L-alanine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-asparagine >> D-Lactate;L-Lactate;L-asparagine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-glutamate D-Lactate;L-Lactate;L-glutamic >> acid;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-glutamine >> D-Lactate;L-Lactate;L-glutamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-glycine >> D-Lactate;L-Lactate;L-glycine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-isoleucine >> D-Lactate;L-Lactate;L-isoleucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-leucine >> D-Lactate;L-Lactate;L-leucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-methionine >> D-Lactate;L-Lactate;L-methionine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-phenylalanine >> D-Lactate;L-Lactate;L-phenylalanine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-proline >> D-Lactate;L-Lactate;L-proline;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-serine >> D-Lactate;L-Lactate;L-serine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-L-threonine >> D-Lactate;L-Lactate;L-threonine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-N-acetyl-D-glucosamine >> D-Lactate;L-Lactate;N-acetyl-D-glucosamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-Adenosine >> D-Lactate;L-Lactate;Phosphate;Sulfate;adenosine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-Putrescine >> D-Lactate;L-Lactate;Phosphate;Sulfate;putrescine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> CN-N-acetyl-D-glucosamine >> N-acetyl-D-glucosamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> P-Cytidine-5-monophosphate D-Lactate;L-Lactate;NH4+;Sulfate;cytidine >> 5' >> monophosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> P-Glycerol-3-phosphate D-Lactate;L-Lactate;NH4+;Sulfate;glycerol >> 3-phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> P-O-phosphoryl-ethanolamine >> D-Lactate;L-Lactate;NH4+;Sulfate;o-phosphoryl-ethanolamine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> P-Tripolyphosphate >> D-Lactate;L-Lactate;NH4+;Sulfate;tripolyphosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Cysteine >> Cysteine;D-Lactate;L-Lactate;NH4+;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Glutathione >> D-Lactate;L-Lactate;NH4+;glutathione;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Hypotaurine >> D-Lactate;L-Lactate;NH4+;hypotaurine;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Sulfate >> D-Lactate;L-Lactate;NH4+;Sulfate;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Sulfite >> D-Lactate;L-Lactate;NH4+;sulfite;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Thiosulfate >> D-Lactate;L-Lactate;NH4+;thiosulfate;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ >> S-Thiourea >> D-Lactate;L-Lactate;NH4+;thiourea;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe >

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KBase Metabolic Modeling Bootcamp: Friday 1-3PM central time
by Christopher Henry 14 Feb '13

14 Feb '13

Hello everyone, We will be holding a KBase Modeling Bootcamp tomorrow (Friday) from 1-3PM central time. As we have done previously, we will hold the bootcamp on webex. The meeting connection information is below. Also, as previously, I would like to offer a conference call number for people to use for audio. The conference call number will be: US/CAN Toll Free: 1-888-850-4523 Participant Passcode: 913601 Don't use the webex number. Please be aware, I am RECORDING these bootcamps (audio and screen cast) for posting online. In this boot camp, we will use IRIS: http://140.221.84.183/iris/Iris/# And we will use the new improved workspace browser: http://140.221.92.49/new/ So load up your phenotype data… warm up your Globus KBase account… pick out your favorite genome, and get ready to have some modeling fun!!! And bring a notebook and sharpened pencils… because I definitely want feedback. Sorry for the late notice. If you can't make it to this one, not to fear. There will be many many more. Best regards, Chris > > > Hi, > > > Christopher Henry is inviting you to this WebEx meeting: > > KBase Metabollic Modeling Bootcamp > Fri, Feb 15, 1:00 pm | 2 hr > Chicago (Central Standard Time, GMT-06:00) > Host: Christopher Henry > > Join > > > Add the attached iCalendar (.ics) file to your calendar. > > Agenda > > This meeting does not have an agenda. > > Access Information > > Where: WebEx Online > Meeting number: 196 404 043 > Password: This meeting does not require a password. > > Audio Connection > > 1-650-479-3207 US TOLL > Access code: 196 404 043 > > Meeting Files (0) > > Can't access your meeting? Get help. > Delivering the power of collaboration, > Cisco WebEx Team > > IMPORTANT NOTICE: This WebEx service includes a feature that allows audio and any documents and other materials exchanged or viewed during the meeting to be recorded. By joining this meeting, you automatically consent to such recordings. If you do not consent to the recording, discuss your concerns with the meeting host prior to the start of the recording or do not join the meeting. Please note that any such recordings may be subject to discovery in the event of litigation. > > ©2012 Cisco and/or its affiliates. All rights reserved. > MT-A-001 >

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Re: [Microbe] Demo data
by Paramvir Dehal 14 Feb '13

14 Feb '13

Hey Chris, I'll take care of the BLAST'ing Paramvir On Thu, Feb 14, 2013 at 9:37 AM, Christopher Henry <chrisshenry(a)gmail.com>wrote: > Hi all, > > So I have a couple of really URGENT requests for data and help I need with > the Adam D. demo. > > 1.) I need a list of ALL paralogs in the g.20848 genome (related to mutant > phenotype analysis) > -Please blast all g.20848 genes against the g.20848 genome and > provide me with a list of all hits > -The list should have two columns: gene ID and blast score (and > other blast metrics) > > 2.) I need a list of ALL hits between genes in the g.20848 genome and > genomes in KBase (related to mutant phenotype analysis) > -Provide me with a four column list: gene ID in g.20848, gene ID > of hit in other genome, annotation of gene we hit, blast score, maybe other > blast metrics > > 3.) MOST URGENT: I had issues with the wild type conditions Ben sent > (related to IMMEDIATE phenotype analysis) > -you gave me 100 conditions, but there were many repeated > conditions (any idea why???) > -You gave me some conditions that had no phosphate source at all > > I translated your wild type conditions into 60 media formulations (listed > below). In the list below, the name of the media is in the first column, > and the full list of compounds is in the second column. The prefix in the > media name reflects my understanding of the study: > "C-" means a study of carbon source > "N-" means a study of nitrogen source > "CN-" means a single compound serving as carbon and nitrogen source > "P-" means phosphate source > "S-" means sulfate source > > Note, I actually had to change three of your conditions because there was > no phosphate source at all. But now I'm uncertain how these correspond to > your knockout phenotypes. Can you resend me the knockout phenotype data > specified in terms of my media names below? And can you send it today > (ASAP)? If I have it by tonight, everything will be done tomorrow. > > Chris > > P.S. I understand (well… really really hope!) there are services in KBase > to get me (1) and (2), and I'd love to hear about them. HOWEVER, please > also run the commands yourself and send me the requested data directly… I > need to try and shave time wherever possible. > > P.P.S. All work is being conducted in workspace "phenotypeDemo" > > C-Butyrate > Butyrate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-Cytidine > Cytidine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-Lactate > D-Lactate;L-Lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-D-Lactate > D-Lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-Guanosine > Guanosine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-Inosine > Inosine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-L-glutamate L-glutamic > acid;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-L-glutamine > L-glutamine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-L-isoleucine > L-isoleucine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-L-lactate > L-lactate;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-L-leucine > L-leucine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-L-serine > L-serine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-N-acetyl-D-glucosamine > N-acetyl-D-glucosamine;NH4+;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-acetate > NH4+;Phosphate;Sulfate;acetate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-adenosine > NH4+;Phosphate;Sulfate;adenosine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-alpha-ketoglutarate NH4+;Phosphate;Sulfate;alpha ketoglutaric > acid;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-gly-asp-L > NH4+;Phosphate;Sulfate;gly-asp-L;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-gly-glu-L > NH4+;Phosphate;Sulfate;gly-glu-L;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-malate NH4+;Phosphate;Sulfate;malic > acid;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-propionate > NH4+;Phosphate;Sulfate;propionate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-pyruvate > NH4+;Phosphate;Sulfate;pyruvate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > C-Uridine > NH4+;Phosphate;Sulfate;Uridine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-Cytidine > Cytidine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-glutamate L-glutamic > acid;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-glutamine > L-glutamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-isoleucine > L-isoleucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-serine > L-serine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-threonine > L-threonine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-Aspartate Aspartic > acid;D-Lactate;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-Arginine > D-Lactate;L-Arginine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-Asparagine > D-Lactate;L-Asparagine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-Glycine > D-Lactate;L-Glycine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-Histidine > D-Lactate;L-Histidine;L-Lactate;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-alanine > D-Lactate;L-Lactate;L-alanine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-asparagine > D-Lactate;L-Lactate;L-asparagine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-glutamate D-Lactate;L-Lactate;L-glutamic > acid;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-glutamine > D-Lactate;L-Lactate;L-glutamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-glycine > D-Lactate;L-Lactate;L-glycine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-isoleucine > D-Lactate;L-Lactate;L-isoleucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-leucine > D-Lactate;L-Lactate;L-leucine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-methionine > D-Lactate;L-Lactate;L-methionine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-phenylalanine > D-Lactate;L-Lactate;L-phenylalanine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-proline > D-Lactate;L-Lactate;L-proline;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-serine > D-Lactate;L-Lactate;L-serine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-L-threonine > D-Lactate;L-Lactate;L-threonine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-N-acetyl-D-glucosamine > D-Lactate;L-Lactate;N-acetyl-D-glucosamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-Adenosine > D-Lactate;L-Lactate;Phosphate;Sulfate;adenosine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-Putrescine > D-Lactate;L-Lactate;Phosphate;Sulfate;putrescine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > CN-N-acetyl-D-glucosamine > N-acetyl-D-glucosamine;Phosphate;Sulfate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > P-Cytidine-5-monophosphate D-Lactate;L-Lactate;NH4+;Sulfate;cytidine > 5' > monophosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > P-Glycerol-3-phosphate D-Lactate;L-Lactate;NH4+;Sulfate;glycerol > 3-phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > P-O-phosphoryl-ethanolamine > D-Lactate;L-Lactate;NH4+;Sulfate;o-phosphoryl-ethanolamine;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > P-Tripolyphosphate > D-Lactate;L-Lactate;NH4+;Sulfate;tripolyphosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > S-Cysteine > Cysteine;D-Lactate;L-Lactate;NH4+;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > S-Glutathione > D-Lactate;L-Lactate;NH4+;glutathione;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > S-Hypotaurine > D-Lactate;L-Lactate;NH4+;hypotaurine;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > S-Sulfate > D-Lactate;L-Lactate;NH4+;Sulfate;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > S-Sulfite > D-Lactate;L-Lactate;NH4+;sulfite;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > S-Thiosulfate > D-Lactate;L-Lactate;NH4+;thiosulfate;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+ > S-Thiourea > D-Lactate;L-Lactate;NH4+;thiourea;Phosphate;Al;Boron;Ca2+;Cl-;Co2+;Cu2+;Fe2+;Fe3+;H+;H2O;K+;Mg;Mn2+;Ni2+;Molybdate;Na+;O2;Zn2+

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