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 (Pf) Post load genome (Pf) Comparative Genomics Global PlasmoDB Workflow [Comp Genomics Dir] Mask Top Level Genome (Pf) Download Files (Pf) [Taxo n] [SO] Load Geno me (Pf) Post- genome (Pf) [Comp Genomic s Dir] Mask Top Level Genome (Pf) Download Files (Pf) [Taxo n] [SO] Load Geno me (Pf) Post- genome (Pf) [Comp Genomic s Dir] Mask Top Level Genome (Pf) Download Files (Pf) [Taxo n] [SO] Load Geno me (Pf) Post- genome (Pf) [Comp Genomic s Dir] Mask Top Level Genome (Pf) Download Files (Pf) [Taxo n] [SO] Load Geno me (Pf) Post- genome (Pf) [Comp Genomic s Dir] Mask Top Level Genome (Pf) Download Files (Pf) [Taxo n] [SO] Load Geno me (Pf) Post- genome (Pf) [Comp Genomic s Dir] Mask Top Level Genome (Pf) Download Files (Pf)

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 Isolates Vocabulary Resource Global This is an optional subgraph reference

4. Init Workflow Home Dir on Cluster Init apiSiteFiles WebServices Dirs Common Init Comparative Genomics Fasta Dir How does rest of flow know where these dirs are? Init apiSiteFiles DownloadSite Dir

5. Make Data Dir Organism-specific ISF Extract Genome Sequence Extract Protein Sequence Mirror Data Dir to Cluster Standard Load Genome Need a slide for this graph

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 fasta to Comp Genome Dir Extract Top Level Fasta

7. Post load genome Genome Analysis Proteome Analysis Run Tuning Manager Organism Specific Workflow Make apiSiteFiles DownloadSite Organism Dir

8. Find Tandem Repeats Load Tandem Repeats Copy Genomic Seqs to Cluster [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 Load GeneGenomicSequence

9. Calculate AASeq Attributes Filter Seqs Load Low Complexity Seqs [NRDB Resource] BLASTP NRDB Psipred [Interpro Resource] InterproScan Run TMHMM Load TMHMM Run SignalP Load SignalP Epitopes [NRDB Resource] Find Seq Identity to NRDB Load NRDB xrefs [PDB Resource] BLASTP PDB Run ExportPred Load ExportPred IEDB Resource IEDB DBxRef Resource Proteome Analysis Make Data Dir

10. Map SAGE Tags to Genome Seqs Pfalciparum SNPs Anti-codon Resource Map Oligos DeRisi oligos Resource Pf SAGE Tag Resource Pf SAGE Tag Freqs Resource [Isolates Resources] Map Isolates to Genome [MO Resource] Microarray Resources DBxRefs Resources Misc Resources [GO Resource] [GO Ev Code Resource] Load GO Association Correct Gene Alias Resource Pfalciparum ChIP-Chip Make Gene Alias Mapping File Pfalciparum specific [EnzymeDB Resource] Load EC Association Make Data Dir Make Eupath_UniProt_Link File

11. 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

12. Greg’s script Pfalciparum ChIP-Chip Load All ChIP- Chip Peaks Check with John B and Greg Henk Stunnenberg Get & Analyze ChIP-Chip Artur Scherf Get & Analyze ChIP-Chip Till Voss Get & Analyze ChIP-Chip Load All ChIP-Chip Smoothed Profiles

13. Plasmodium Isolates Resources Genbank Isolates Resource

14. Pfalciparum ISF Resources P.falciparum_chromosomes Resource

15. Pfalciparum EST Resources ZhangGardnerPf3D7_EstLibrary Resource WatanabePf3D7_PredictedTranscripts Resource WatanabePf3D7_EstLibrary Resource Florent_ESTLibrary Resource

16. 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

17. Pfalciparum Misc Resources Su_P.falciparum_Mic rosatellite_Markers Resource loadPfLocationMap WithSqlldr Resource Evigan Resource PlasmoMap_Intera ctome Resource PhylogeneticProfi les_Pfalciparum Resource MutualInformatio nScores_Pfalcipa rum Resource pfChrsGenBank DbRefs Resource ecMappings_Hag ai Resource pathwayMappings _Hagai 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 Pfalciparum_RN A_Seq Resource RodentPlasmod iumChromosom es Resource P.falciparum_old _annotations Resource updateEviganSe condaryScore Resource y2h_data Resource

18. 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

19. Pfalciparum Microarray Resources derisi_time_series Resource winzeler_cell_cycle Resource winzeler_gametocyte_e xpression Resource Cowman_radAnalysis Resource DOZI_array Resource daily_array Resource ……

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

21. 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

22. 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

23. 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

24. Extract Genomic Seqs into Separate Fasta Files Make Data Dir Make Gf Client Cluster Task Input Dir Mirror Gf Client to Cluster Mirror Gf Client From Cluster [Blat Quality Scores] Insert BLAT Alignment Setbest BLAT Alignment Start GFCluster Task Wait for GF Cluster Task Run Nib On Cluster Map Assembly Seqs to Genome

25. 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

26. Make Data Dir Make Assembly Gf Client Cluster Task Input Dir Mirror Assembly Gf Client to Cluster Start GF Task on Cluster Wait for GF Cluster Task Mirror Gf Client From Cluster [Blat Quality Scores] Insert BLAT Alignment Setbest BLAT Alignment Update Assembly Source Id Map Assemblies to Genome

27. 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

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

29. 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

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

31. Get and Analyze ChIP-Chip ChIP-Chip Resource Make Data Dir Map Probe to Genome Load Mapping Results Load Probe Profiles

32. 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

33. 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

34. 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

35. 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

36. 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

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

38. Run MercatorMavid Make Mercator Gff File Correct Reading Frame in Mercator Gff file Mercator Make Data Dir Make GFF Data Dir Copy files to Web Svc Dir