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Legend. Make Data Dir. = Step. Global. = Subgraph call. Load Genomic Sequence & Annotation. = Subgraph reference. Proteome Analysis. = Optional step. = Global dependency. [Taxon] Pk ISF.

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  1. Legend Make Data Dir = Step Global = Subgraph call Load Genomic Sequence & Annotation = Subgraph reference Proteome Analysis = Optional step = Global dependency [Taxon] Pk ISF Note: in many of the following slides the titles are hyperlinks to the associated XML file. (Right click on the title and select Open Hyperlink.)

  2. PlasmoDB Workflow Common Global [Taxon] [SO] Load Genome P.falciparum Post load genome (Pf) Mask Top Level Genome (Pf) Organism Specific (Pf) Load And Correct Gene Aliases (Pf) Organism Specific (top-level) Load DbxRefs (Pf) Download Files (Pf) Comparative Genomics .htaccess file

  3. Global Make Data Dir Init User/Group/Project BlatAlignmentQuality Resource GO Resource NRDB Resource PDB Resource Taxonomy Resource SO Resource Mged Ontology Resource EnzymeDB Resource GO Evidence Codes Resource InterPro Resource Init Workflow Home Dir on Cluster This is an optional subgraph reference Update PDB Taxon Isolates Resources Mirror To Cluster

  4. Common Init apiSiteFilesWebServices Blast Dir Init apiSiteFilesWebServicesMtof Dir Init apiSiteFilesWebServices Mercator Dir Init Comparative Genomics Gff Dir Init Comparative Genomics Fasta Dir

  5. Standard Load Genome Make Data Dir Make apiSiteFilesDownloadSite Organism Dir Organism-specific ISF Insert Organism Project Extract Genomic Seqs into Separate Fasta Files Extract Genome Sequence Extract Protein Sequence Fix File Names for Separate Fasta Extract genome Fasta for Short Seq Aligner Extract Gene Models file for Short Seq Aligner Extract transcript Fasta for Short Seq Aligner Make Genome Target List File Bowtie Index for Genome Bowtie Index for Trascripts Mirror Data Dir to Cluster Run Nib On Cluster

  6. Make and Mask Top Level Genome Make Data Dir AGP virtual seq Tuning Mgr Extract Top Level Fasta Make Mercator Gff File Make Cluster Task Input Dir Correct Reading Frame in Mercator Gff file Mirror To Cluster Start Repeat Mask Cluster Task Copy Corrected Gff File to Comp Genome Dir Wait for Cluster Task Mirror From Cluster Copy Masked fasta to Comp Genome Dir

  7. Post load genome Make Data Dir Mirror Data Dir to Cluster Genome Analysis Proteome Analysis Run Tuning Manager

  8. Genome Analysis Make Data Dir tRNA Scan [NRDB Resource] BLASTX NRDB dbEST Resource Organism-specific EST Resources Document tRNA Scan Document BLAST NRDB Make and Block Candidate Assem Seqs Filter Sequences Make ORFs Load Low Complexity Seqs Document Low Complexity Map Candidate Assem Seqs to Genome Find Tandem Repeats Make and Block DoTS Assemblies Load Tandem Repeats Document Tandem Repeats Load ORFs Document ORFs Map DoTS Assemblies to genome Mass Spec Resources

  9. Proteome Analysis Make Data Dir Load GeneGenomicSequence [NRDB Rsrc] BLASTP NRDB [PDB Rsrc] BLASTP PDB [Interpro Resource] InterproScan Document Interpro Document BLAST PDB Document BLAST NRDB Calculate AASeq Attributes Load Product name [NRDB Rsrc] Seq Identity to NRDB Filter Seqs [NRDB Resource] Psipred Run SignalP Load NRDB xrefs Load Low Complexity Seqs Document SignalP Load SignalP Document Low Comp Document PsiPred IEDB Resource Run TMHMM Run ExportPred Document TMHMM Load TMHMM Epitopes IEDB DBxRef Resource Document Export Pred Load ExportPred

  10. Pfalciparum specific Make Data Dir Mirror To Cluster [EnzymeDB Resource] Load EC Association [Isolates Resources] Map Isolates to Genome [GO Resource] [GO Ev Code Resource] Load GO Association Pf Array Studies Pfalciparum SNPs Pf RNAseq and ChIPseq Misc Resource Anti-codon Resource Pf SAGE Tag Resource Pf PiggyBac Resource Mirror To Cluster Map SAGE Tags to Genome Seqs Pf SAGE Tag Freqs Resource Pf Map PiggyBac to Genome Seqs

  11. Pfalciparum ISF Resources Make Data Dir P.falciparum_chromosomesResource Pfalciparum_mitResource Pfalciparum_apicoplastResource Pfalciparum_previous aliasesResource

  12. Pfalciparum SNPs Make Data Dir Broad Get & Analyze SNPs Su Get & Analyze SNPs Winzeler Get & Analyze SNPs Sanger Pf Get & Analyze SNPs Sanger Pr Get & Analyze SNPs Combined Get & Analyze SNPs XSu Get & Analyze SNPs Broad Isolate Barcode Resource Broad 3K Genotyping Resource Broad 75K Genotyping Resource

  13. Pfalciparum EST Resources Make Data Dir ZhangGardnerPf3D7_EstLibrary Resource WatanabePf3D7_PredictedTranscripts Resource WatanabePf3D7_EstLibrary Resource Florent_ESTLibrary Resource

  14. Pfalciparum Mass Spec Resources Make Data Dir Florens_Life_Cycle_MassSpec_Mrz Resource Florens_Life_Cycle_MassSpec_Gmt Resource Lasonder_Mosquito_Oocysts_Mass_Spec Resource Florens_Life_Cycle_MassSpec_Spz Resource Lasonder_Mosquito_oocyst_derived_sporozoites Resource Florens_Life_Cycle_MassSpec_Tpz Resource Lasonder_Mosquito_salivary_gland_sporozoites Resource Florens_PIESPs_MassSpec Resource P.falciparum_Clinical_Proteomics Resource Pf_Merozoite_Peptides Resource

  15. Pfalciparum RNAseq and ChIPseq Make Data Dir Duffy RNAseq Newbold RNAseq LeRoch ChIPseq

  16. Rename “probe” to “array element” Pfalciparum Array Studies (1) SCR Malaria Get and Map probes Winzeler Cell Cycle Experiment Resource Winzeler GametocyteExperiment Resource Daily Experiment Resource Cowman Sir2 KO Experiment Resource Cowman Invasion KO Experiment Resource Cowman Sir2 KO Analyze Microarray Expression Cowman Invasion KO Analyze Microarray Expression Winzeler Cell Cycle Analyze Microarray Expression Winzeler Gametocyte Analyze Microarray Expression Daily Analyze Microarray Expression DeRisi Get and Map probes Different derisi experiments use different arrayelement sets. Can we combine these? DeRisi 3D7 Experiment Resource DeRisi HB3 Experiment Resource DeRisi Dd2 Experiment Resource DeRisi HB3 Analyze Microarray Expression DeRisi Dd2 Analyze Microarray Expression DeRisi 3D7 Analyze Microarray Expression

  17. Pfalciparum Array Studies (2) GPL8808 Get and Map Probes A-MEXP-75 Get and Map probes Affy-pf-sanger Get and Map probes Affy-pf-anaphelse Get and Map probes A-MEXP-1407 Get and Map Probes Voss Experiment Resource E-MEXP-128 Experiment Resource NewBoldExperiment Resource E-GEOD-10022 Experiment Resource Scherf Experiment Resource Voss Analyze ChIP-Chip E-MEXP-128 Analyze Microarray Expression NewBoldAnalyze Microarray Expression E-GEOD-10022 Analyze Microarray Expression Scherf Analyze ChIP-Chip 9981A_3D7-H4K20me3-wt Scherf Analyze ChIP-Chip 9981A_3D7-H3K9me3-wt Scherf Analyze ChIP-Chip 9981_3D7-H3K9me3-wt Scherf Analyze ChIP-Chip 9435B_3D7-H4K20me3-wt Winzeler Westenberger Get and Map Probes Scherf Analyze ChIP-Chip 9435B_3D7-H3K9me3-wt Scherf Analyze ChIP-Chip 9435B_3D7-H3K9Ac-wt Scherf Analyze ChIP-Chip 9435B_3D7-H3K4me3-wt Scherf Analyze ChIP-Chip 9435A_3D7-H3K9me3-sir2KO Winzeler Westenberger Experiment Resource Scherf Analyze ChIP-Chip 9435A_3D7-H3K9Ac-wt Scherf Analyze ChIP-Chip 9435A_3D7-H3K9Ac-sir2KO Scherf Analyze ChIP-Chip 9435A_3D7-H3K4me3-wt Scherf Analyze ChIP-Chip 14070B_3D7-H3K9me3-sir2KO Scherf Analyze ChIP-Chip 14070B_3D7-H3K9Ac-sir2KO Winzeler WestenbergerAnalyze ChIP-Chip Troph nucleosome Winzeler WestenbergerAnalyze ChIP-Chip schizont Winzeler WestenbergerAnalyze ChIP-Chip ring Winzeler WestenbergerAnalyze ChIP-Chip troph

  18. Pf LeRoch ChIPseq Make Data Dir LeRoch ChIPseq Resource Analyze Sample MAINE0 Analyze Sample MAINE6 Analyze Sample MAINE12 Analyze Sample MAINE18 Analyze Sample MAINE24 Analyze Sample MAINE30 Analyze Sample MAINE36 Analyze Sample FAIRE0 Analyze Sample FAIRE6 Analyze Sample FAIRE12 Analyze Sample FAIRE18 Analyze Sample FAIRE24 Analyze Sample FAIRE30 Analyze Sample FAIRE36

  19. Pf Duffy RNAseq Coverage file maker includes normalization and adding sample name column Make Data Dir Duffy RNAseq Resource Make Samples Data Dir Analyze RNAseq sample PL02 Analyze RNAseq sample 3D7 Analyze RNAseq sample PL01 Merge intensity files make percentile file Load intensity and percentile profile

  20. Pf Newbold RNAseq Make Data Dir Newbold RNAseq Resource Make Samples Data Dir Analyze RNAseq sample Hour 0 Analyze RNAseq sample Hour 8 Analyze RNAseq sample Hour 16 Analyze RNAseq sample Hour 24 Analyze RNAseq sample Hour 32 Analyze RNAseq sample Hour 40 Analyze RNAseq sample Hour 48 Merge intensity files make percentile file Load intensity and percentile profile

  21. Pfalciparum DBxRefs Resources Make Data Dir ecMappings_Hagai Resource pfChrsGenBankDbRefs Resource P.falciparum_chromosomes_xRefs Resource Entrez_Gene_dbxref Resource Winzeler_Literature_References Resource SGPPMapping Resource Entrez_DBRefs Resource winzeler_westenberger_dbrefs Resource predictedProteinStructures Resource Plasmodraft_DBRefs Resource Phenotype_DBRefs Resource PlasmoMAP_DBRefs Resource MR4Reagents Resource BRENDAMapping Resource Pubmed_DBRefs Resource PASA_DBRefs Resource Uniprot_Gene_dbxref Resource y2h_data Resource PlasmoMap_Interactome Resource MutualInformationScores_Pfalciparum Resource pathwayMappings_Hagai Resource Make Eupath_UniProt_Link File

  22. Pfalciparum Misc Resources Make Data Dir Su_P.falciparum_Microsatellite_Markers Resource P.falciparum_old_annotations Resource Cowman_Subcellular_motifs Resource Broad_SNP_coverage Resource BrickMAPPpromoters Resource Haldar_Subcellular_motifs Resource loadMAPPWithSqlldr Resource loadPfLocationMapWithSqlldr Resource PhylogeneticProfiles_Pfalciparum Resource ApicoplastTargeting Resource Pf_Gene_Aliases Resource Evigan Resource updateEviganSecondaryScore Resource

  23. Pf Map PiggyBac to Genome Seqs Make data dir Make Task Input Dir Mirror Data Dir to Cluster Start blast on Cluster Wait for cluster Copy files From cluster Convert Blast Result To Gff Fille Load Result Gff File

  24. Pchabaudi specific Make Data Dir Mirror To Cluster [Isolates Resources] Map Isolates to Genome [GO Resource] [GO Ev Code Resource] Load GO Association [EnzymeDB Resource] Load EC Association Misc Resources

  25. Pchabaudi DBxRefs Resources Make Data Dir pc_Entrez_DBRefs Resource Pc_Phenotype_DBRefs Resource pc_Pubmed_DBRefs Resource pc_Entrez_Gene_dbxref Resource pc_Uniprot_Gene_dbxref Resource

  26. Pchabaudi Misc Resources Make Data Dir TransFactorBindingSites _Llinas Resource

  27. Pberghei specific Make Data Dir Mirror To Cluster [GO Resource] [GO Ev Code Resource] Load GO Association [EnzymeDB Resource] Load EC Association [Isolates Resources] Map Isolates to Genome Misc Resources PbArray Studies

  28. Pberghei Mass Spec Resources Make Data Dir Waters_female_gametes Resource Waters_mixed_gametes Resource Waters_male_gametes Resource Pberghei_Protein_Expression Experiment Resource

  29. Pberghei DBxRefs Resources Make Data Dir pb_Entrez_DBRefs Resource Pb_Phenotype_DBRefs Resource pb_Pubmed_DBRefs Resource pb_Entrez_Gene_dbxref Resource pb_Uniprot_Gene_dbxref Resource

  30. Pberghei Array Studies Make Data Dir GSS cDNA Array Get and Map probes DOZI long oligoes Get and Map probes gss_time_series HP Experiment Resource gss_time_series HPE Experiment Resource DOZI Experiment Resource DOZI Analyze Microarray Expression gss_time_series HP Analyze Microarray Expression gss_time_series HPE Analyze Microarray Expression

  31. PbergheiEST Resources Make Data Dir WatanabePbANKA_PredictedTranscripts Resource

  32. Pberghei Misc Resources Make Data Dir TransFactorBindingSites _Llinas Resource

  33. Pknowlesi specific Make Data Dir Mirror To Cluster [GO Resource] [GO Ev Code Resource] Load GO Association [EnzymeDB Resource] Load EC Association [Isolates Resources] Map Isolates to Genome Misc Resources

  34. Pknowlesi DBxRefs Resources Make Data Dir pk_Pubmed_DBRefs Resource pk_Entrez_Gene_dbxref Resource pk_Uniprot_Gene_dbxref Resource pk_Entrez_DBRefs Resource

  35. Pknowlesi Misc Resources Make Data Dir TransFactorBindingSites _Llinas Resource

  36. Pgallinaceum specific Make Data Dir Mirror To Cluster [Isolates Resources] Map Isolates to Genome

  37. Preichenowi specific Make Data Dir Mirror To Cluster [Isolates Resources] Map Isolates to Genome

  38. Pvivax specific Make Data Dir Mirror To Cluster [GO Resource] [GO Ev Code Resource] Load GO Association [EnzymeDB Resource] Load EC Association [Isolates Resources] Map Isolates to Genome PvArray Studies Misc Resources

  39. Pvivax Mass Spec Resources Make Data Dir P.vivax_Clinical_Proteomics Resource

  40. Pvivax DBxRefs Resources Make Data Dir pv_Entrez_DBRefs Resource Pv_Phenotype_DBRefs Resource pv_Pubmed_DBRefs Resource pv_Entrez_Gene_dbxref Resource pv_Uniprot_Gene_dbxref Resource P.vivax_DBRefs Resource P.vivax_sequenceGB_DBRefsResource

  41. Pvivax Array Studies Make Data Dir PvivaxOligoFromZB Get and Map probes PvivaxLib520507 Get and Map probes ZB_Time_Series Experiment Resource Westenberger Experiment Resource ZB_Time_Series Analyze Microarray Expression Westenberger Analyze Microarray Expression

  42. PvivaxEST Resources Make Data Dir WatanabePv_PredictedTranscripts Resource WatanabePv_EstLibrary Resource

  43. Pvivax Misc Resources Make Data Dir TransFactorBindingSites _Llinas Resource

  44. Pyoelii specific Make Data Dir Mirror To Cluster [EnzymeDB Resource] Load EC Association Misc Resources [Isolates Resources] Map Isolates to Genome PyArray Studies [GO Resource] [GO Ev Code Resource] Load GO Association

  45. Pyoelii Mass Spec Resources Make Data Dir Pyoelii_LiverStage_LS40 Resource Pyoelii_LiverStage_LS50 Resource

  46. Pyoelii Misc Resources Make Data Dir PhylogeneticProfiles_Pyoelii Resource TransFactorBindingSites _Llinas Resource

  47. Pyoelii DBxRefs Resources Make Data Dir MutualInformationScores_Pyoelii Resource py_Entrez_DBRefs Resource py_Pubmed_DBRefs Resource py_Entrez_Gene_dbxref Resource py_Uniprot_Gene_dbxref Resource

  48. Pyoelii Array Studies Make Data Dir Vaidya_Bergman_oligos Get and Map probes SCR Malaria Get and Map probes winzelerPyPfCom Experiment Resource Kappe Experiment Resource KappeAnalyze Microarray Expression winzelerPyPfCom Analyze Microarray Expression

  49. PyoeliiEST Resources Make Data Dir WatanabePy17XL_PredictedTranscripts Resource WatanabePy17XL_EstLibrary Resource

  50. Plasmodium Isolates Resources Make Data Dir Genbank Isolates Resource Isolates Vocabulary Resource Isolates Continent Resource Update Isolation Source Resource Update Specific Host Resource Update Geographic Location Resource Update Product Resource

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