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.)

Common

[Taxon][SO]Load

Genome

Post load genome

(Pf)

ComparativeGenomics

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

Init User/Group/Project

Make Data Dir

TaxonomyResource

GOResource

BlatAlignmentQuality Resource

NRDBResource

PDBResource

EnzymeDBResource

SOResource

InterProResource

GOEvidence

CodesResource

Update PDB Taxon

Mged OntologyResource

IsolatesResources

Global

This is an optional subgraph reference

Mirror To Cluster

Init Workflow Home Dir on

Cluster

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

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

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

MakeData 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

Post load genome

Genome Analysis

ProteomeAnalysis

Run Tuning Manager

Make Data Dir

Mirror Data Dir to Cluster

Find Tandem Repeats

Load Tandem Repeats

[NRDB Resource]BLASTXNRDB

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

genomeMass SpecResources

dbESTResource

Organism-specific EST Resources

Make Data DirGenome Analysis

Document BLAST NRDB

Document tRNA Scan

Document ORFs

Document Tandem Repeats

Document Low

Complexity

Calculate AASeq

Attributes

Filter Seqs

Load Low Complexity

Seqs

[NRDB Rsrc]BLASTPNRDB

[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

IEDBResource

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

Map SAGE Tags to

Genome Seqs

PfalciparumSNPs

Anti-codonResource

Pf SAGE TagResource

Pf SAGE Tag FreqsResource

[Isolates Resources] Map Isolates to

Genome

Pf Array Studies

MiscResource

[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 PiggyBacResource

Mirror To Cluster

Pfalciparum ISF Resources

P.falciparum_chromosomes Resource

Pfalciparum_mit ResourcePfalciparum_apicoplast

Resource

Make Data Dir

Pfalciparum_previous aliases Resource

Su Get & Analyze

SNPs

Broad Get & Analyze

SNPs

Winzeler Get & Analyze

SNPs

Sanger PfGet & Analyze

SNPs

Sanger PrGet & Analyze

SNPs

CombinedGet & Analyze

SNPs

Broad Isolate

BarcodeResource

Broad 3K GenotypingResource

Pfalciparum SNPs

Broad 75K GenotypingResource

Make Data Dir

XSu Get & Analyze

SNPs

Pfalciparum EST Resources

ZhangGardnerPf3D7_EstLibrary Resource

WatanabePf3D7_PredictedTranscripts Resource

WatanabePf3D7_EstLibrary Resource

Florent_ESTLibraryResource

Make Data Dir

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

Pfalciparum RNAseq and ChIPseq

Newbold RNAseq

Make Data Dir

Duffy RNAseq

LeRoch ChIPseq

Pfalciparum Array Studies (1)SCR MalariaGet and Map

probes

Winzeler Cell Cycle

ExperimentResource

Winzeler Cell Cycle Analyze

MicroarrayExpression

Winzeler GametocyteExperimentResource

Winzeler Gametocyte

Analyze MicroarrayExpression

Daily ExperimentResource

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 ExperimentResource

DeRisi Dd2 Analyze

Microarray Expression

DeRisi 3D7 ExperimentResource

DeRisi 3D7 Analyze

MicroarrayExpression

DeRisi HB3 ExperimentResource

DeRisi HB3 Analyze

Microarray Expression

Cowman Sir2 KO

ExperimentResource

Cowman Sir2 KO Analyze Microarray Expression

Cowman Invasion KO ExperimentResource

Cowman Invasion KO

Analyze Microarray Expression

Pfalciparum Array Studies (2)A-MEXP-75Get and Map

probes

E-MEXP-128 ExperimentResource

E-MEXP-128 Analyze

Microarray Expression

Affy-pf-sangerGet and Map

probes

NewBold ExperimentResource

NewBold Analyze

Microarray Expression

Affy-pf-anaphelse

Get and Map probes

E-GEOD-10022 ExperimentResource

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 WestenbergerGet and Map

Probes

WinzelerWestenberger

Analyze ChIP-Chipschizont

Winzeler Westenberger Experiment Resource

WinzelerWestenberger

Analyze ChIP-Chip

ring

WinzelerWestenberger

Analyze ChIP-Chip

troph

WinzelerWestenberger

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-Chip9981_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

LeRoch ChIPseq Resource

Make Data Dir

AnalyzeSampleMAINE0

Pf LeRoch ChIPseq

AnalyzeSample MAINE6

AnalyzeSample

MAINE12

AnalyzeSample

MAINE18

AnalyzeSample

MAINE24

AnalyzeSample

MAINE30

AnalyzeSample

MAINE36

AnalyzeSample FAIRE0

AnalyzeSample FAIRE6

AnalyzeSample

FAIRE12

AnalyzeSample

FAIRE18

AnalyzeSample

FAIRE24

AnalyzeSample

FAIRE30

AnalyzeSample

FAIRE36

Pf Duffy RNAseq Make Data Dir

Coverage file maker includes normalization 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

Pf Newbold RNAseq Make Data Dir

Newbold RNAseq

Resource

Analyze RNAseq sampleHour 0

Analyze RNAseq sampleHour 8

Analyze RNAseq sampleHour 16

Merge intensity files

Load intensity and percentile

profile

Make Samples Data Dir

make percentile file

Analyze RNAseq sampleHour 32

Analyze RNAseq sampleHour 40

Analyze RNAseq sampleHour 48

Analyze RNAseq sampleHour 24

Pfalciparum DBxRefs Resources

P.falciparum_chromosomes_xRefsResource

Entrez_DBRefsResource

Phenotype_DBRefsResource

Pubmed_DBRefsResource

Entrez_Gene_dbxrefResource

Uniprot_Gene_dbxref

Resource

PASA_DBRefsResource

PlasmoMAP_DBRefs

Resource

winzeler_westenberger_dbrefsResource

Winzeler_Literature_ReferencesResource

predictedProteinStructures

Resource

MR4ReagentsResource

BRENDAMappingResource

SGPPMappingResource

Plasmodraft_DBRefs

Resource

Make Eupath_UniProt_Link

File

y2h_dataResource

PlasmoMap_Interactome

Resource

MutualInformationScores_Pfalciparum

Resource

pathwayMappings_Hagai

Resource

pfChrsGenBankDbRefs

Resource

ecMappings_Hagai

Resource

Make Data Dir

Pfalciparum Misc Resources

Su_P.falciparum_Microsatellite_Markers

Resource

loadPfLocationMapWithSqlldrResource

EviganResource

PhylogeneticProfiles_Pfalciparum

Resource

Cowman_Subcellular_motifsResource

Haldar_Subcellular_motifs

Resource

ApicoplastTargeting

Resource

Broad_SNP_coverage

Resource

BrickMAPPpromoters

Resource

loadMAPPWithSqlldr

Resource

Pf_Gene_AliasesResource

P.falciparum_old_annotations

Resource

updateEviganSecondaryScore

Resource

Make Data Dir

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

[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

MiscResources

Pchabaudi DBxRefs Resources

pc_Pubmed_DBRefs Resource

pc_Entrez_Gene_dbxref Resource

pc_Uniprot_Gene_dbxref Resource

pc_Entrez_DBRefsResource

Pc_Phenotype_DBRefsResource

Make Data Dir

Pchabaudi Misc Resources

Make Data Dir

TransFactorBindingSites _Llinas Resource

[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

MiscResources

Pberghei Mass Spec Resources

Waters_male_gametes Resource

Waters_female_gametes Resource

Waters_mixed_gametes Resource

Make Data Dir

Pberghei_Protein_Expression Experiment

Resource

Pberghei DBxRefs Resources

pb_Pubmed_DBRefs Resource

pb_Entrez_Gene_dbxref Resource

pb_Uniprot_Gene_dbxref Resource

pb_Entrez_DBRefsResource

Pb_Phenotype_DBRefsResource

Make Data Dir

Pberghei Array Studies

DOZI ExperimentResource

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 oligoesGet and Map

probes

Pberghei EST Resources

WatanabePbANKA_PredictedTranscripts Resource

Make Data Dir

Pberghei Misc Resources

Make Data Dir

TransFactorBindingSites _Llinas Resource

[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

MiscResources

Pknowlesi DBxRefs Resources

pk_Pubmed_DBRefs Resource

pk_Entrez_Gene_dbxref Resource

pk_Uniprot_Gene_dbxref Resource

pk_Entrez_DBRefsResource

Make Data Dir

Pknowlesi Misc Resources

Make Data Dir

TransFactorBindingSites _Llinas Resource

[Isolates Resources] Map Isolates to

Genome

Pgallinaceum specific

Make Data Dir

Mirror To Cluster

[Isolates Resources] Map Isolates to

Genome

Preichenowi specific

Make Data Dir

Mirror To Cluster

[Isolates Resources] Map Isolates to

GenomePv Array Studies

[GO Resource] [GO Ev Code Resource]

Load GO Association

Pvivax specific

[EnzymeDB Resource] Load EC Association

Make Data Dir

Mirror To Cluster

MiscResources

Pvivax Mass Spec Resources

P.vivax_Clinical_Proteomics Resource

Make Data Dir

Pvivax DBxRefs Resources

pv_Pubmed_DBRefs Resource

pv_Entrez_Gene_dbxref Resource

pv_Uniprot_Gene_dbxref Resource

pv_Entrez_DBRefsResource

Pv_Phenotype_DBRefsResource

P.vivax_DBRefs Resource

P.vivax_sequenceGB_DBRefsResource

Make Data Dir

Pvivax Array Studies

ZB_Time_Series ExperimentResource

ZB_Time_Series Analyze Microarray Expression

PvivaxOligoFromZBGet and Map probes

WestenbergerExperimentResource

Westenberger Analyze Microarray Expression

PvivaxLib520507 Get and Map probes

Make Data Dir

Pvivax EST Resources

WatanabePv_PredictedTranscripts Resource

Make Data Dir

WatanabePv_EstLibrary Resource

Pvivax Misc Resources

Make Data Dir

TransFactorBindingSites _Llinas Resource

[Isolates Resources] Map Isolates to

Genome

Py Array Studies

MiscResources

[GO Resource] [GO Ev Code Resource]

Load GO Association

Pyoelii specific

[EnzymeDB Resource] Load EC Association

Make Data Dir

Mirror To Cluster

Pyoelii Mass Spec Resources

Pyoelii_LiverStage_LS50 Resource Pyoelii_LiverStage_LS40

Resource

Make Data Dir

Pyoelii Misc Resources

PhylogeneticProfiles_Pyoelii Resource

Make Data Dir

TransFactorBindingSites _Llinas Resource

Pyoelii DBxRefs Resources

py_Pubmed_DBRefs Resource

py_Entrez_Gene_dbxref Resource

py_Uniprot_Gene_dbxref Resource

py_Entrez_DBRefsResource

MutualInformationScores_Pyoelii Resource

Make Data Dir

Pyoelii Array Studies

Kappe ExperimentResource

Kappe Analyze Microarray Expression

Vaidya_Bergman_oligosGet and Map probes

Make Data Dir

winzelerPyPfCom Experiment Resource

winzelerPyPfCom Analyze

Microarray Expression

SCR MalariaGet and Map

probes

Pyoelii EST Resources

WatanabePy17XL_PredictedTranscripts

Resource

Make Data Dir

WatanabePy17XL_EstLibrary Resource

Plasmodium Isolates Resources

Genbank Isolates

Resource

Isolates VocabularyResource

Update Product Resource

Update Geographic

Location Resource

Update Specific Host Resource

Update Isolation Source

Resource

Isolates ContinentResource

Make Data Dir

Get and Map Array Elements

ArrayResource

ShortSeqAligner

Load probe genome Mapping

Results

Make Data Dir

Make probe-gene mapping file

Make .cdf file

Make probe genome Mapping

Gff File

Run Parse2fastagive proper sequence

ids to probe setsRevert probe sequence Id

Transcript expression script

Analyze Microarray Expression Experiment

Insert Analysis ResultInsert Expression

Profile

Make Data Dir

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

Analyze ChIPseq or RNAseq Sample

ShortSeqAligner

Load Coverage File

Compute Peaks

Load Peaks

Make Data Dir

Make And Normalize

Coverage File

Reformat Coverage FileMake Intensities

File

SSA

SSA Bowtie Just Genome

Find unmapped seqs

SSA BLAT

Merge Bowtie and BLAT

SSA BowtieGenome And Transcripts

Make Data Dir

Remove trailing mismatches

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

SSA Bowtie

Run Bowtie

Make genome unique and non-

unique files

Make Data Dir

SSA BLAT

Run mdust

Transform files into blatu and

blatnu files

Make Data Dir

Blat Against genome

Load Resource

Make data dir

Run Plugin

GetAndUnpack

Insert Ext Db Rls

Insert Ext Db

BLAST Make data dir

Start blast on Cluster

Wait for cluster

Copy files From cluster

extract IDsFrom Blast

result

Load Subjectsubset

Load Result

Optional steps(runtime test)

filter by subject

Mirror Data Dir to Cluster

Make Task Input Dir

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

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

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

Make Data Dir

[Blat Quality Scores]Insert BLAT Alignment

Setbest BLAT Alignment

Map Assembly Seqs to Genome

Blat Against genome

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

Make Data Dir

[Blat Quality Scores]Insert BLAT Alignment

Setbest BLAT Alignment

Update Assembly Source Id

Map Assemblies to Genome

Blat Against genome

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

Epitopes

Make Data Dir

Make Blast Dir

Format NCBI blast file

Create Epitoptes map file

Load Epitopes map

Psipred

fix protein IDsFor psipred

create psipredTask dir

copy Data Dirto cluster

start psipredOn cluster

wait for cluster

copy psipredFiles from

cluster

fix psipredFile names

make Alg Inv

load psipred

run pfilt on nrdb

Make data dir

Extract Isolate Seqs

Copy Isolate Seqs to Cluster

BLAST Isolates Against Genome

Map Isolates to Genome

Make Data Dir

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

Run Mummer

Convert Mummer Result to Gff file

Load Mummer Resoult

SNPResource

Extract Fasta file from Gff file

Get and Analyze SNPsMake Data Dir

Extract Annotated Transcript

SeqsExtract 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

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

Make EST Download

File

Format EST

Download File

Make assembly Download

File

Format assemblyDownload

File

Make dot CDS

Download File

Format CDS

Download File

Make dot transcript Download

File

Format transcriptDownload

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

OrthoMCL phyletic profiles

Resource

OrthoMCL orthologous groups

Resource

Comparative Genomics

MakeData Dir

Run Mercator

Insert Mercator Synteny Spans

Tuning Mgr

RodentPlasmodiumChromosomes

Resource

Run MercatorMavid

Mercator

MakeData Dir

Copy files to Web Svc Dir