1 / 38

Legend

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

cisco
Download Presentation

Legend

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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 (Pf) [Taxon] [SO] Load Genome (Pf) [Taxon] [SO] Load Genome (Pf) [Taxon] [SO] Load Genome (Pf) [Taxon] [SO] Load Genome (Pf) [Taxon] [SO] Load Genome (Pf) Post load genome (Pf) [Comp Genomics Dir] Mask Top Level Genome (Pf) Post-genome (Pf) [Comp Genomics Dir] Mask Top Level Genome (Pf) Post-genome (Pf) [Comp Genomics Dir] Mask Top Level Genome (Pf) [Comp Genomics Dir] Mask Top Level Genome (Pf) Post-genome (Pf) [Comp Genomics Dir] Mask Top Level Genome (Pf) Post-genome (Pf) [Comp Genomics Dir] Mask Top Level Genome (Pf) Post-genome (Pf) Download Files (Pf) Download Files (Pf) Download Files (Pf) Download Files (Pf) Download Files (Pf) Download Files (Pf) Comparative Genomics

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

  4. Common How does rest of flow know where these dirs are? Init Workflow Home Dir on Cluster Init apiSiteFilesDownloadSite Dir Init apiSiteFilesWebServicesDirs Init Comparative Genomics Fasta Dir

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

  6. Make and Mask Top Level Genome Make Data Dir AGP virtual seq Tuning Mgr Extract Top Level Fasta Make Cluster Task Input Dir Mirror To Cluster Start Repeat Mask Cluster Task Wait for Cluster Task Mirror From Cluster Copy fasta to Comp Genome Dir

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

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

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

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

  11. Pfalciparum SNPs 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 Broad Isolate Barcode Resource Broad 3K Genotyping Resource Broad 75K Genotyping Resource

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

  13. Plasmodium Isolates Resources Genbank Isolates Resource

  14. Pfalciparum ISF Resources P.falciparum_chromosomesResource

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

  16. Pfalciparum Mass Spec Resources 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

  17. Pfalciparum Misc Resources Su_P.falciparum_Microsatellite_Markers Resource PhylogeneticProfiles_Pfalciparum Resource pathwayMappings_Hagai Resource Broad_SNP_coverage Resource Pfalciparum_RNA_Seq Resource loadPfLocationMapWithSqlldr Resource MutualInformationScores_Pfalciparum Resource Cowman_Subcellular_motifs Resource BrickMAPPpromoters Resource RodentPlasmodiumChromosomes Resource y2h_data Resource pfChrsGenBankDbRefs Resource Haldar_Subcellular_motifs Resource loadMAPPWithSqlldr Resource P.falciparum_old_annotations Resource PlasmoMap_Interactome Resource ecMappings_Hagai Resource ApicoplastTargeting Resource Pf_Gene_Aliases Resource Evigan Resource updateEviganSecondaryScore Resource

  18. Pfalciparum DBxRefs Resources P.falciparum_chromosomes_xRefs Resource Entrez_Gene_dbxref Resource Winzeler_Literature_References Resource SGPPMapping Resource Entrez_DBRefs Resource Uniprot_Gene_dbxref Resource predictedProteinStructures Resource Plasmodraft_DBRefs Resource Phenotype_DBRefs Resource PlasmoMAP_DBRefs Resource MR4Reagents Resource BRENDAMapping Resource Pubmed_DBRefs Resource PASA_DBRefs Resource winzeler_westenberger_dbrefs Resource

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

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

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

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

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

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

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

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

  27. InterproScan 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

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

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

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

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

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

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

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

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

  36. Make And Format Download Files Gene detail table and file Sequence detail table and file Gff cache and file Make EST Download File Make assembly Download File Make dot CDS Download File Make dot transcript Download File Make proteins Download File Make genomic Download File Make ORF Download File Make Interpro Download File Make ORF NA Download File Make CondonUsage Download File Format EST Download File Format assemblyDownload File Format CDS Download File Format transcriptDownload File Format proteins Download File Format Genomic Download File Format ORF Download File

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

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

More Related