1. Legend Global = Subgraph call Make Data Dir = Step Load Genomic Sequence & Annotation = Subgraph reference Proteome Analysis = Optional step [Taxon] Pk ISF = Global dependency 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. Common [Taxon] [SO] Load Genome Post load genome (Pf) Comparative Genomics Global PlasmoDB Workflow Mask Top Level Genome (Pf) Download Files (Pf) Load DbxRefs (Pf) Organism Specific (Pf) Load And Correct Gene Aliases (Pf) P.falciparum Organism Specific (top-level).htaccess file

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

4. Common Init Comparative Genomics Fasta Dir Init Comparative Genomics Gff Dir Init apiSiteFiles WebServices Mtof Dir Init apiSiteFiles WebServices Blast Dir Init apiSiteFiles WebServices Mercator Dir

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

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

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

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

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

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

11. Pfalciparum ISF Resources P.falciparum_chromosomes Resource Pfalciparum_mit Resource Pfalciparum_apicoplast Resource Make Data Dir Pfalciparum_previous aliases Resource

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

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

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

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

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

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

18. LeRoch ChIPseq Resource Make Data Dir Analyze Sample MAINE0 Pf LeRoch ChIPseq 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 Make Data Dir Coverage file maker includes normalizati on and adding sample name column Duffy RNAseq Resource Analyze RNAseq sample PL01 Analyze RNAseq sample PL02 Analyze RNAseq sample 3D7 Merge intensity files Load intensity and percentile profile Make Samples Data Dir make percentile file

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

21. Pfalciparum DBxRefs Resources P.falciparum_chromos omes_xRefs Resource Entrez_DBRefs Resource Phenotype_DBRefs Resource Pubmed_DBRefs Resource Entrez_Gene_dbxref Resource Uniprot_Gene_dbxre f Resource PASA_DBRefs Resource PlasmoMAP_DBRef s Resource winzeler_westenber ger_dbrefs Resource Winzeler_Literature_ References Resource predictedProteinStru ctures Resource MR4Reagents Resource BRENDAMapping Resource SGPPMapping Resource Plasmodraft_DBRe fs Resource Make Eupath_UniProt_Link File y2h_data Resource PlasmoMap_Interacto me Resource MutualInformationSco res_Pfalciparum Resource pathwayMappings _Hagai Resource pfChrsGenBank DbRefs Resource ecMappings_Hag ai Resource Make Data Dir

22. Pfalciparum Misc Resources Su_P.falciparum_Mic rosatellite_Markers Resource loadPfLocationMap WithSqlldr Resource Evigan Resource PhylogeneticProfi les_Pfalciparum Resource Cowman_Subcellu lar_motifs Resource Haldar_Subcellula r_motifs Resource ApicoplastTargetin g Resource Broad_SNP_cov erage Resource BrickMAPPprom oters Resource loadMAPPWithS qlldr Resource Pf_Gene_Aliases Resource P.falciparum_old _annotations Resource updateEviganSe condaryScore Resource Make Data Dir

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

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

25. Pchabaudi DBxRefs Resources pc_Pubmed_DBRefs Resource pc_Entrez_Gene_db xref Resource pc_Uniprot_Gene_d bxref Resource pc_Entrez_DBRefs Resource Pc_Phenotype_DBRefs Resource Make Data Dir

26. Pchabaudi Misc Resources Make Data Dir TransFactorBindingSites _Llinas Resource

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

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

29. Pberghei DBxRefs Resources pb_Pubmed_DBRefs Resource pb_Entrez_Gene_db xref Resource pb_Uniprot_Gene_d bxref Resource pb_Entrez_DBRefs Resource Pb_Phenotype_DBRefs Resource Make Data Dir

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

31. P berghei EST Resources WatanabePbANKA_PredictedTranscripts Resource Make Data Dir

32. Pberghei Misc Resources Make Data Dir TransFactorBindingSites _Llinas Resource

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

34. Pknowlesi DBxRefs Resources pk_Pubmed_DBRefs Resource pk_Entrez_Gene_db xref Resource pk_Uniprot_Gene_d bxref Resource pk_Entrez_DBRefs Resource Make Data Dir

35. Pknowlesi Misc Resources Make Data Dir TransFactorBindingSites _Llinas Resource

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

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

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

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

40. Pvivax DBxRefs Resources pv_Pubmed_DBRefs Resource pv_Entrez_Gene_db xref Resource pv_Uniprot_Gene_d bxref Resource pv_Entrez_DBRefs Resource Pv_Phenotype_DBRefs Resource P.vivax_DBRefs Resource P.vivax_sequenceGB _DBRefsResource Make Data Dir

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

42. P vivax EST Resources WatanabePv_PredictedTranscripts Resource Make Data Dir WatanabePv_EstLibrary Resource

43. Pvivax Misc Resources Make Data Dir TransFactorBindingSites _Llinas Resource

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

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

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

47. Pyoelii DBxRefs Resources py_Pubmed_DBRefs Resource py_Entrez_Gene_db xref Resource py_Uniprot_Gene_d bxref Resource py_Entrez_DBRefs Resource MutualInformationSc ores_Pyoelii Resource Make Data Dir

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

49. P yoelii EST Resources WatanabePy17XL_PredictedTranscripts Resource Make Data Dir WatanabePy17XL_EstLibrary Resource

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

51. Get and Map Array Elements Array Resource ShortSeqAligner Load probe genome Mapping Results Make Data Dir Make probe-gene mapping file Make.cdf file Make probe genome Mapping Gff File Run Parse2fasta give proper sequence ids to probe sets Revert probe sequence Id

52. Transcript expression script Analyze Microarray Expression Experiment Insert Analysis Result Insert Expression Profile Make Data Dir

53. Run ChIPChip Peak Finder Analyze ChIPchip Sample Load ChIP-Chip Peak Scores Reformat ChIP-Chip Smoothed Profiles File Load Chip-chip Peak Features Make Data Dir Transform raw data to genome coordinates Make Peak Finder Data Dir Generate ChIP-Chip Peak Feature Gff File Reformat ChIP-Chip Peak Scores File Load ChIP-Chip Smoothed Profiles Transform adds column for unique probe ids. For averaged probes, just use one

54. Analyze ChIPseq or RNAseq Sample ShortSeqAligner Load Coverage File Compute Peaks Load Peaks Make Data Dir Make And Normalize Coverage File Reformat Coverage File Make Intensities File

55. SSA SSA Bowtie Just Genome Find unmapped seqs SSA BLAT Merge Bowtie and BLAT SSA Bowtie Genome And Transcripts Make Data Dir Remove trailing mismatches

56. SSA Bowtie Genome & Transcriptome Ssa Bowtie against Genome Merge gu and tu into bowtie unique merge gnu and tnu and cnu into bowtie non- unique Ssa Bowtie against Transcripts Make Data Dir

57. SSA Bowtie Run Bowtie Make genome unique and non- unique files Make Data Dir

58. SSA BLAT Run mdust Transform files into blatu and blatnu files Make Data Dir Blat Against genome

59. Load Resource Make data dir Run Plugin GetAndUnpack Insert Ext Db Rls Insert Ext Db

60. BLAST Make data dir Start blast on Cluster Wait for cluster Copy files From cluster extract IDs From Blast result Load Subject subset Load Result Optional steps (runtime test) filter by subject Mirror Data Dir to Cluster Make Task Input Dir

61. BLAT Against Genome Make Gf Client Cluster Task Input Dir Mirror Gf Client to Cluster Mirror Gf Client From Cluster Start GFCluster Task Wait for GF Cluster Task FIx Genome Source Ids In Blat Result File

62. TRNA Scan Make data dir Start TRNA Scan Wait for cluster Copy files From cluster Mirror Data Dir to Cluster Make Task Input Dir Load TRNA Scan

63. Make Candidate Assembly Seqs Extract Candidate Assembly Seqs Make Cluster Task Input Dir Mirror To Cluster Start Repeat Mask Cluster Task Wait for Cluster Task Mirror From Cluster Make Data Dir Make Candidate Assembly Seqs from Predicted Transcripts Optional steps (runtime test) Make and Block Assembly Seqs

64. Make Data Dir [Blat Quality Scores] Insert BLAT Alignment Setbest BLAT Alignment Map Assembly Seqs to Genome Blat Against genome

65. Cluster Transcripts by Genome Alignment Put Unaligned Transcripts into One Cluster Assemble Transcripts Extract Assemblies Make Data Dir Make Repeat Mask Cluster Task Input Dir Mirror Assembly Repeat Mask To Cluster Start RM Task on Cluster Wait for RM Cluster Task Make and Block Assemblies

66. Make Data Dir [Blat Quality Scores] Insert BLAT Alignment Setbest BLAT Alignment Update Assembly Source Id Map Assemblies to Genome Blat Against genome

67. Make Data Dir Make InterproScan Cluster Task Input Dir Mirror InterproScan to Cluster Start Cluster Task Wait for Cluster Task Mirror InterproScan From Cluster Insert IprScan Results InterproScan

68. Epitopes Make Data Dir Make Blast Dir Format NCBI blast file Create Epitoptes map file Load Epitopes map

69. Psipred fix protein IDs For psipred create psipred Task dir copy Data Dir to cluster start psipred On cluster wait for cluster copy psipred Files from cluster fix psipred File names make Alg Inv load psipred run pfilt on nrdb Make data dir

70. Extract Isolate Seqs Copy Isolate Seqs to Cluster BLAST Isolates Against Genome Map Isolates to Genome Make Data Dir

71. Extract BAC Ends Seqs Map BAC Ends Seqs to Genome Make Data Dir Make Repeat Mask Cluster Task Input Dir Mirror BAC ENDs Repeat Mask To Cluster Start RM Task on Cluster Wait for RM Cluster Task Map BAC Ends Seqs to Genome Seqs

72. Run Mummer Convert Mummer Result to Gff file Load Mummer Resoult SNP Resource Extract Fasta file from Gff file Get and Analyze SNPs Make Data Dir

73. Extract Annotated Transcript Seqs Extract Oligo Seqs Copy Transcripts Seqs to Cluster Copy Oligo Seqs to Cluster BLAST Oligo Against Transcripts BLAST Oligo Against Genomic Seqs Map Oligos Make Data Dir

74. Load SAGE Tag Mapping Results Create SAGE Tag Normalization Files Load SAGE Tag Normalization Results Extract SAGE Tag Seqs Map SAGE Tag seqs to Genome Seqs Map SAGE Tags to Genome Seqs Make Data Dir

75. Make EST Download File Format EST Download File Make assembly Download File Format assembly Download File Make dot CDS Download File Format CDS Download File Make dot transcript Download File Format transcript Download File Make proteins Download File Format proteins Download File Make genomic Download File Format Genomic Download File Make ORF Download File Format ORF Download File Make ORF NA Download File Make Interpro Download File Make CondonUs age Download File Gene detail table and file Sequence detail table and file Gff cache and file Make And Format Download Files Format Expression Profile Download File

76. OrthoMCL phyletic profiles Resource OrthoMCL orthologous groups Resource Comparative Genomics Make Data Dir Run Mercator Insert Mercator Synteny Spans Tuning Mgr RodentPlasmodiumC hromosomes Resource

77. Run MercatorMavid Mercator Make Data Dir Copy files to Web Svc Dir