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

14 Feb '13

Hi Chris, You are correct. I accidentally left the phosphate out of all the variable sulfur-source media definitions. While fixing this, I noticed another typo regarding CAS amino acids. The attached sheet should be corrected (wild type only). Note, I have not corrected the KO sheet yet. I'll send that later today. Unless there is some major reason, I would like to keep the naming of the experiments as it is in the first column of the attached sheet. These names match Morgan and Adam's original sheet and I use them to check for errors. 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 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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Demo data
by Christopher Henry 14 Feb '13

14 Feb '13

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] Reminder: microbes call today
by Davison, Brian H. 11 Feb '13

11 Feb '13

Paul Wrong phone # 866-740-1260 4958182 code -----Original Message----- From: microbe-bounces(a)lists.kbase.us [mailto:[email protected]] On Behalf Of Christopher Henry Sent: Monday, February 11, 2013 2:06 PM To: Paul Frybarger Cc: KBase Microbes List Subject: Re: [Microbe] Reminder: microbes call today Working fine for me. Try connecting again. Chris On Feb 11, 2013, at 1:02 PM, Paul Frybarger <pfrybarger(a)gmail.com> wrote: > I'm having trouble connecting. There is nothing but silence when I call. Is anyone else experiencing this? > > - Paul > > > On Mon, Feb 11, 2013 at 12:16 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Hey everyone, > > We've got a call today at 11am P / 1pm Central > > 18664951270 > 4958182 > > > > _______________________________________________ > 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 _______________________________________________ Microbe mailing list Microbe(a)lists.kbase.us https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] Reminder: microbes call today
by Christopher Henry 11 Feb '13

11 Feb '13

Working fine for me. Try connecting again. Chris On Feb 11, 2013, at 1:02 PM, Paul Frybarger <pfrybarger(a)gmail.com> wrote: > I'm having trouble connecting. There is nothing but silence when I call. Is anyone else experiencing this? > > - Paul > > > On Mon, Feb 11, 2013 at 12:16 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Hey everyone, > > We've got a call today at 11am P / 1pm Central > > 18664951270 > 4958182 > > > > _______________________________________________ > 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: microbes call today
by Paul Frybarger 11 Feb '13

11 Feb '13

I'm having trouble connecting. There is nothing but silence when I call. Is anyone else experiencing this? - Paul On Mon, Feb 11, 2013 at 12:16 PM, Paramvir Dehal <psdehal(a)lbl.gov> wrote: > Hey everyone, > > We've got a call today at 11am P / 1pm Central > > 18664951270 > 4958182 > > > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe > >

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Reminder: microbes call today
by Paramvir Dehal 11 Feb '13

11 Feb '13

Hey everyone, We've got a call today at 11am P / 1pm Central 18664951270 4958182

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Fwd: Invitation to WebEx meeting: Christopher Henry's WebEx Meeting
by Christopher Henry 08 Feb '13

08 Feb '13

Webex information to connect to modeling bootcamp. I do plan to record the meeting (my screen video and audio), so if that's a problem, let me know. Begin forwarded message: > From: Christopher Henry via Cisco WebEx <admin(a)webex.com> > Subject: Invitation to WebEx meeting: Christopher Henry's WebEx Meeting > Date: February 8, 2013 11:01:01 AM CST > To: chrisshenry(a)gmail.com > Reply-To: marland(a)mcs.anl.gov > > > Hi, > > > Christopher Henry is inviting you to this WebEx meeting: > > Christopher Henry's WebEx Meeting > Fri, Feb 8, 12:00 pm | 2 hr 30 min > Chicago (Central Standard Time, GMT-06:00) > Host: Christopher Henry > > Join > > > Add the attached iCalendar (.ics) file to your calendar. > > Agenda > > Modeling bootcamp > > Access Information > > Where: WebEx Online > Meeting number: 196 305 116 > Password: This meeting does not require a password. > > Audio Connection > > None > > 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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