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Let’sgotoouragendatoday!
Pleasegotothewebsite:https://joslynnlee.github.io/2017-05-25-GSLI/
ChangesandmostlyonlineJ
WhatisCyVerse?
• CyberinfrastructurefortheUniverse• NSFFundedproject• Providestorageandcomputing• Large-scaleanalysisandbigdata• Educationalresources• Atmosphere:Cloud-Computing
Recapofsamplecollectionsites
Needtounderstandalittlemoreaboutthissoitallmakessense!
MetadataisessentialOrganizefilenames
BoomtoBust:ResultedinAbandonment
• Abandonedmineshavebeenleakingtoxicacidmineralwasteintothestreams
• Federalandstateofficialsestimatethatabout1,500gallonsofacidminedrainageadayflowintotheriverfromtheseSilverton-areamines.
• GoldKingMinehadbeenleaking200gallonsofwasteaminutebeforetheEPAcrewbegandiggingtoinvestigatethesource.
https://www.abqjournal.com/941984/dont-blame-epa-for-gold-king-spill.html
EPAexplainswhathappened• TheAugust2015spillattheGoldKingMineinsouthwesternColorado
released3milliongallonsofwastewatertaintedwithiron,aluminum,manganese,lead,copperandothermetals.RiversinColorado,NewMexicoandUtahwerepolluted,withstretchesofwaterwayturninganeerieorange-yellow.
• Whileexcavatingabovetheoldadit,pressurizedwaterbeganleakingabovetheminetunnel,spillingaboutthreemilliongallonsofwaterstoredbehindthecollapsedmaterialintoCementCreek,atributaryoftheAnimasRiver.
• EPAtakesresponsibilityfortheGoldKingMinereleaseandiscommittedtocontinueworkinghand-in-handwiththeimpactedlocalgovernments,statesandtribes.
https://www.epa.gov/goldkingmine/follow-monitoring-data-gold-king-mine-incidenthttps://www.epa.gov/goldkingmine%20
YellowminewastewateratentrancetotheGKMonAug.5
Environmental Protection Agency via Reutershttps://www.washingtonpost.com/news/morning-mix/wp/2015/08/10/what-the-epa-was-doing-when-it-sent-yellow-sludge-spilling-into-a-colorado-creek/?utm_term=.6d8369e091d3
TimelineofwastehittingvarioustownsinCO/NM/AZ
August5
AztecAug7
FarmingtonAug8
Shiprock Aug10
LakePowellAug14
Twodaysamplecollection,7sites
• Day 1o Gold King Mine, Silverton, COo Baker’s Bridge, Animas River, Hermosa, COo FLC Bathroom, Durango, CO
• Day 2o San Juan River (not affected), Bloomfield, NMo San Juan River, Upper Fruitland, NMo San Juan River (canal), Nenahnezad, NMo San Juan River, Hogback, NMo Skate Park, Animas River, Durango, CO
Firstsite:GoldKingMine(GKM)SiteSamplinginsidetreatmentcenter
Pre-treatedwater Filterafterrunningpre-treatedwater
Sedimentsamplecollectionofsludge
GoldKingMinewatertreatmentplant,pretreatmentwaterpipe,estimatedpH5.8GoldKingMinewatertreatmentplant,posttreatment[flocculant Drewfloc 2499addedforwatertreatment]
Secondsite:Baker’sBridge(BB)sitenorthofDurango
Outdoorlab:pumpset-up Dr.Lowellwasoursedimentcollector.
Secondsite:Baker’sBridge(BB)sitenorthofDurango
March2017 May2017
Lower water level earlier this year
Fourthsite:Bloomfield(BLM)NMandSanJuanRiver(beforeAnimasRiver)
Publicsite:RiverwalknearbridgeRiverwaterappearedturbid;clogged2filters;locationisSanJuanRiverbeforejoiningofAnimasRiver
Fourthsite:UpperFruitland(UF)beginningofNavajoNation
AfterAnimasRiverjoinsSanJuan,NNcanalsystembegins
CanalstartinUpperFruitlandChapter
Fifthsite:Nenahnezad (NZ)canalonNavajoNation
Canallocation:DivertwaterupstreamforfarmsandreturnstoSanJuanRiver
SedimentcollectionatdroppointbyTaraandJacob
Fifthsite:Nenahnezad (NZ)canalonNavajoNation
Truck Lab: Brandon demonstrating the processWater was easier to
collect at drop point
Seventhsite:AnimasRiverDurango(DRO)location
Rocksinthearea
Waterneartheskatepark
Murkyriverwaterbeforebridge
DNAExtractionatDNALC,Sendoffforsequencing!
Powersoil tubes(smallerthanPowerWater)extractDNA
Firstcleaning
Introducestudentstometadata• Metadataisstructuredinformationthatdescribes,explains,locates,orotherwisemakesiteasiertoretrieve,use,ormanageaninformationresource.Metadataisoftencalleddataaboutdataorinformationaboutinformation.
• Samplecollection:o GPSlocationo Temperatureo Windo pHo controls
**Iwillprepareasheetwithinformation
UnderstandingMetadata,NationalInformationStandardsOrganization
INPUT:Sequencereadformat• Knowwhatformyoursequencingreadscomein• A.fastq formatstoresbothanucleotidesequenceanditscorrespondingqualityscores.
• A.fastq filenormallyusesfourlinespersequence:
@SRR2146911.11length=78ACGAGTGCGTTTAGATAACCTGGTAGCTAGCTCAGTACGAGACTGCCAAGGAAGTCGTAACAAGGTAACTAGCTCAGT+SRR2146911.11length=78IIIIIIIHD666?IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHCCCCIIIIIIIIIIIIIIIIIIIIIIIIIII@SRR2146911.22length=66ACGAGTGCGTATTAGATACCCGGTAGCTAGCTCAGTACTAAGTCGTAACAAGGTACCTAGCTCAGT+SRR2146911.22length=66FFFHHHHHHIEBBBDE<5/////50/17<<<?AAAD??<99;<?;8445////76;<<:;;[email protected]=55ACGAGTGCGTATTAGATACCCAGGTAGGAAGTCGTAACAAGGTACCTAGCTCAGT+SRR2146911.33length=55IIIIIIIIIIFFDBGHD:///7449<////<CD?>>571133CFAAB>AAADFDG
INPUT:Sequencereadformat
Line1beginswitha'@'characterandisfollowedbyasequenceidentifierandanoptionaldescription(likeaFASTAtitleline)Line2istherawsequencelettersLine3beginswitha'+'characterandisoptionallyfollowedbythesamesequenceidentifier(andanydescription)again.Line4encodesthequalityvaluesforthesequenceinLine2,andmustcontainthesamenumberofsymbolsaslettersinthesequence.
@SRR2146911.11length=78ACGAGTGCGTTTAGATAACCTGGTAGCTAGCTCAGTACGAGACTGCCAAGGAAGTCGTAACAAGGTAACTAGCTCAGT+SRR2146911.11length=78IIIIIIIHD666?IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIHHCCCCIIIIIIIIIIIIIIIIIIIIIIIIIII@SRR2146911.22length=66ACGAGTGCGTATTAGATACCCGGTAGCTAGCTCAGTACTAAGTCGTAACAAGGTACCTAGCTCAGT+SRR2146911.22length=66FFFHHHHHHIEBBBDE<5/////50/17<<<?AAAD??<99;<?;8445////76;<<:;;[email protected]=55ACGAGTGCGTATTAGATACCCAGGTAGGAAGTCGTAACAAGGTACCTAGCTCAGT+SRR2146911.33length=55IIIIIIIIIIFFDBGHD:///7449<////<CD?>>571133CFAAB>AAADFDG
16SrRNA AnalysisPlatforms
• Bioinformaticstools,manyoptions• QIIME– (canonicallypronouncedchime)standsforQuantitativeInsightsIntoMicrobialEcology
• open-sourcebioinformaticspipelineforperformingmicrobiome analysisfromrawDNAsequencingdata
• Writteninpython
16SrRNA genedatabasestoclassifysequences
Greengenes offersannotated,chimera-checked,full-length16SrRNA genesequencesinstandardalignmentformats.
http://aem.asm.org/content/72/7/5069.full
TeachingtoolwithJupyter Notebooks
Thenotebookextendstheconsole-basedapproachtointeractivecomputinginaqualitativelynewdirection,providingaweb-basedapplicationsuitableforcapturingthewholecomputationprocess:developing,documenting,andexecutingcode,aswellascommunicatingtheresults.
http://nbviewer.jupyter.org/github/biocore/qiime/blob/1.9.1/examples/ipynb/illumina_overview_tutorial.ipynb