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Option Type: FILE
Argument: aadimerfreq aadis aafreq aaprop acctable addalias addppi addquery aliases aliasfile altcontrol altdis altpam alttreatment archived arraydata assembly background backupdb basefile batchout biogrid biomart blastd blasti blasto blastopt blastres buildfile cardout compdb control ctlfile cwtree data datout datpickup dbindex ddi dip disin dmidata dmifile domfilter domino domtable dormant elm elmclass elmdat elmdomains elminstance elminteractors elmpfam embldat ensloci equivout errorlog evidence expconvert fam fasdb fastq filexref filterout focus ftfile ftfreq ftgablam ftout gablam gablamdis genbase genecards genemap genepickle genome godata goids gomap haqbat haqdb haqmatrix hgncdata hgncmap hhpid hivseq hmmout hmmtab homeback iini indata infile info intact ipilinks jobini larrow linkout litfile loadmatrix log makedb mapdb mapdna mapseq mascot megaslim mgcfile mgidata mint miranda mitab motifout motifs motinfo msfile mutfile mutpileup namemap nandr negatives netphos newres nsfin obofile occbenchpos occdata occfile occres omim orthdb outfile pairwise pamfile pamout parse pdbdata pelm pelmfas peptides pfam pfamdata phosblast phosres phyoptions picback picdesc pichome pickledata pileup pillars pingupickle positives posmatrix ppi ppifile ppiout preassembly pridefile projects protdesc protdist qblast qryspec qseqfile qslimfinder querydb queryppi queryseq randres randsource rarrow reactome readcheck reference refgenome refseq relcons resfile restin savedis savetree scansite scapback screenddi screenfile searchdb searchini seqdb seqin seqout signalp singlesf slimcheck slimdesc slimres snpfile snpmap snptable source sourcedata specfile spectdt sqldump tabber tabout tagfile tagindex tagmap taxadb taxmap tdtfile titletext tmhmm treatment uniprot unispec validated vnematrix wtpileup xmerback xmerfile xmerseq xref xrefdata
Modules: bob diploidocus humsf09 jrj_fastq orcfinder patis revert rje_1433 rje_aic rje_archive rje_embl rje_genomics rje_hivqsf rje_hm_html rje_hmm_V2 rje_mirna rje_misc rje_omim rje_pacbio rje_paml rje_price rje_slimfungo rje_spf rje_taxamap samphaser scap slimdip slimfrap slimgoer slimjim slimpid trex compass peptide_dismatrix peptide_stats pic_html prodigis rje_dbase rje_glossary rje_mysql rje_pattern_discovery rje_phos rje_scansite rje_seqgen rje_seqplot rje_yeast seqforker sfmap2png slim_pickings wormpump gopher_V2 qslimfinder_V1.9 slimbench_V1 slimfinder_V4.9 slimprob_V1.4 rje_aaprop rje_biogrid rje_blast_V1 rje_blast_V2 rje_blast rje_dismatrix_V2 rje_dismatrix_V3 rje_ensembl rje_genbank rje_genecards rje_genemap rje_go rje_hmm_V1 rje_hpc rje_html rje_iridis rje_markov rje_mascot rje_mitab rje_motiflist rje_obj rje_pam rje_ppi rje_samtools_V0 rje_samtools rje_seqlist rje_seq rje_slimcalc rje_slimcore rje_slimhtml rje_slimlist rje_synteny rje_taxonomy rje_tm rje_tree rje_uniprot rje_xml rje rje_xref snp_mapper aphid badasp budapest comparimotif_V3 fiesta gablam gasp gfessa gopher happi haqesac multihaq pagsat_V1 pagsat peptcluster picsi pingu_V3 pingu_V4 presto_V5 qslimfinder seqmapper slimbench slimfarmer slimfinder slimmutant slimparser slimprob slimsearch smrtscape_V1 smrtscape snapper unifake
| Module | Option | Description | Default |
|---|---|---|---|
| aphid | data=FILE |
Delimited file containing input data | None |
| aphid | seqin=FILE |
Sequence file containing hits (if pepnorm != count) | None |
| badasp | log=FILE |
Redirect log to FILE | Default = calling_program.log or basefile.log |
| badasp | pamfile=FILE |
Sets PAM1 input file | jones.pam |
| bob | motifs=FILE |
File of motifs for selected analysis | |
| bob | newres=FILE |
Name for new results file | *.bob.csv |
| bob | randres=FILE |
File with results of random SLiMFinder runs. Will use for DS significance assessment. | None |
| bob | slimres=FILE |
Name of SLiMFinder results file | |
| budapest | haqdb=FILE |
Optional additional search database for MultiHAQ analysis | None |
| budapest | mascot=FILE |
Name of MASCOT csv file | None |
| budapest | searchdb=FILE |
Fasta file for GABLAM search of EST translations | None |
| budapest | seqin=FILE |
Name of EST fasta file used for search | None |
| comparimotif_V3 | aafreq=FILE |
Use FILE to replace uniform AAFreqs (FILE can be sequences or aafreq) | None |
| comparimotif_V3 | motifs=FILE |
File of input motifs/peptides | None |
| comparimotif_V3 | motinfo=FILE |
Filename for output of motif summary table (if desired) | None |
| comparimotif_V3 | resfile=FILE |
Name of results file, FILE.compare.tdt. | motifsFILE-searchdbFILE.compare.tdt |
| comparimotif_V3 | searchdb=FILE |
(Optional) second motif file to compare. Will compare to self if none given. | None |
| compass | netphos=FILE |
Motif prediction files for sequences in netphos format | *.netphos |
| compass | scansite=FILE |
Motif prediction files for sequences in scansite format | *.scansite, *.automotif & *.elm |
| compass | signalp=FILE |
SignalP results in single-line format | *.signalp |
| compass | tmhmm=FILE |
Transmembrane topology data in TMHMM single-line format | *.tmhmm |
| compass | uniprot=FILE |
Sequence features/details in UniProt download format | *.uniprot |
| diploidocus | basefile=FILE |
Root of output file names | diploidocus |
| fiesta | blastopt=FILE |
File containing additional BLAST options for run, e.g. -B F | None |
| fiesta | querydb=FILE |
File of query sequences to search for in EST library | None |
| fiesta | searchdb=FILE |
Fasta file for GABLAM search of EST translations | None |
| fiesta | seqin=FILE |
EST file to be processed | None |
| gablam | blastres=FILE |
BLAST results file for input (over-rides seqin and searchdb) | None |
| gablam | searchdb=FILE |
Database to search. | By default, same as seqin |
| gablam | seqin=FILE |
Query dataset file | infile.fas |
| gasp | nsfin=FILE |
Newick Standard Format treefile | infile.nsf |
| gasp | seqin=FILE |
Fasta/ClustalW/Phylip Format sequence file | infile.fas |
| gfessa | expconvert=FILE |
File containing 'Header', 'Experiment' conversion data | None |
| gfessa | seqin=FILE |
File containing EST/cDNA data to search for tags within | None |
| gfessa | tagfile=FILE |
File containing SuperSAGE tags and counts | None |
| gfessa | tagindex=FILE |
File containing possible tags and sequence names from seqin file | *.tag.index |
| gfessa | tagmap=FILE |
Tag to sequence mapping file to over-ride auto-generated file based on Seqin and Mismatch | None |
| gopher | orthdb=FILE |
Fasta file with pool of sequences for orthology discovery | |
| gopher | orthdb=FILE |
Fasta file with pool of sequences for orthology discovery | |
| gopher | seqin=FILE |
Fasta file of 'query' sequences for orthology discovery (over-rides uniprotid=LIST) | |
| gopher | unispec=FILE |
UniProt species file for TaxaID conversion. Will use TaxaID instead of Species Code if given | None |
| gopher_V2 | orthdb=FILE |
Fasta file with pool of sequences for orthology discovery | |
| gopher_V2 | orthdb=FILE |
Fasta file with pool of sequences for orthology discovery | |
| gopher_V2 | seqin=FILE |
Fasta file of 'query' sequences for orthology discovery | |
| happi | gablam=FILE |
Delimited GABLAM results file for homology data | basefile.gablam.tdt |
| happi | godata=FILE |
Delimited file of GO Data (Gene,GO_ID,GO_Type,GO_Desc) | basefile.go.tdt |
| happi | indata=FILE |
Input data for front pages | |
| happi | pairwise=FILE |
Pairwise protein-protein interation (PPI) file | |
| happi | titletext=FILE |
File containing (Page,ID,Title) for mouseover text | titletext.tdt |
| happi | xrefdata=FILE |
File of Database cross-references. Must have "Gene" field. | |
| haqesac | fasdb=FILE |
Fasta format database to extract sequences from | None |
| haqesac | haqmatrix=FILE |
File of AA vs AA scores used in SAQ and PAQ. | None |
| haqesac | log=FILE |
Redirect log to FILE | Default = calling_program.log or basefile.log |
| haqesac | pamfile=FILE |
Sets PAM1 input file | jones.pam |
| haqesac | phyoptions=FILE |
File containing extra Phylip tree-making options ('batch running') to use | None |
| haqesac | protdist=FILE |
File containing extra Phylip PROTDIST ('batch running') to use | None |
| haqesac | qblast=FILE |
BLAST database against which to BLAST query (see rje_blast.py options) [None] | 'blaste=1e-7','blastv=1000,blastb=0' |
| haqesac | qseqfile=FILE |
Sequence file from which to extract query (query=X) and peform BLAST | None |
| humsf09 | domtable=FILE |
Table of domain predictions | None |
| humsf09 | elm=FILE |
File of ELM Motifs | None |
| humsf09 | nandr=FILE |
File of Neduva & Russell motifs | None |
| humsf09 | pairwise=FILE |
Pingu Pairwise PPI file | None |
| humsf09 | pickledata=FILE |
Genemap pickle to import and use. (See other rje_genemap options) | None |
| jrj_fastq | basefile=FILE |
Base name for output (input by default) | None |
| jrj_fastq | fastq=FILE |
Input FASTQ file for analysis | None |
| multihaq | seqin=FILE |
Input query sequences | None |
| orcfinder | altdis=FILE |
Alternative all by all distance matrix for relationships | None |
| orcfinder | ftfreq=FILE |
File containing UPC frequencies of relevant feature subcategories | None |
| orcfinder | gablamdis=FILE |
Alternative GABLAM results file | None |
| orcfinder | resfile=FILE |
Main SLiMFinder results table | slimfinder.csv |
| orcfinder | seqin=FILE |
Sequence file to search | None |
| pagsat | assembly=FILE |
Fasta file of assembled contigs to assess | None |
| pagsat | refgenome=FILE |
Fasta file of reference genome for assessment (also *.gb for full functionality) | None |
| pagsat_V1 | assembly=FILE |
Fasta file of assembled contigs to assess | None |
| pagsat_V1 | refgenome=FILE |
Fasta file of reference genome for assessment (also *.gb for full functionality) | None |
| patis | mgcfile=FILE |
Name of the MGC clone sequence file | mgc_clones.human.fasta |
| peptcluster | aadis=FILE |
Alternative amino acid distance matrix | None |
| peptcluster | aaprop=FILE |
File of amino acid properties | aaprop.txt |
| peptcluster | savedis=FILE |
Output distance matrix to file | peptides.* |
| peptcluster | savetree=FILE |
Save generated tree as FILE | peptides.peptdis.peptcluster.* |
| peptide_dismatrix | aaprop=FILE |
Amino Acid property matrix file. | aaprop.txt |
| peptide_stats | aaprop=FILE |
Amino Acid property matrix file. | aaprop.txt |
| pic_html | homeback=FILE |
File to use for picture home background | None |
| pic_html | larrow=FILE |
Image file for Left Arrow (pref GIF) | larrow.gif |
| pic_html | picback=FILE |
File to use for other page backgrounds | None |
| pic_html | picdesc=FILE |
File with picture descriptions Type:Group:Element Description | pic_descriptions.txt |
| pic_html | pichome=FILE |
File name for pictures home page | pictures.htm |
| pic_html | rarrow=FILE |
Image file for Right Arrow (pref GIF) | rarrow.gif |
| picsi | basefile=FILE |
Base for output files | picsi |
| picsi | qryspec=FILE |
Species code for Query species | EMIHU |
| picsi | seqin=FILE |
File containing sequences hit during searches | None |
| picsi | spectdt=FILE |
File of UniProt species translations | '/scratch/RJE_Filestore/SBSBINF/Databases/DBase_090505/UniProt/uniprot.spec.tdt' |
| pingu_V3 | addalias=FILE |
Extra (manual?) aliases to add to GeneMap object following loading of pickles etc. | None |
| pingu_V3 | addppi=FILE |
Add additional PPI from a simple delimited file IDA,IDB,Evidence | None |
| pingu_V3 | biogrid=FILE |
BioGRID flat file | None |
| pingu_V3 | dip=FILE |
DIP interactions flat file | None |
| pingu_V3 | domino=FILE |
Domino interactions flat file | None |
| pingu_V3 | ensloci=FILE |
File of EnsEMBL genome EnsLoci treatment | |
| pingu_V3 | evidence=FILE |
Mapping file for evidence terms | None |
| pingu_V3 | genepickle=FILE |
Pickled GeneMap object. Alternatively, use below commands to make GeneMap object | None |
| pingu_V3 | intact=FILE |
IntAct flat file | None |
| pingu_V3 | ipilinks=FILE |
IPI Links file with 'IPI', 'Symbol' and 'EnsG' fields | |
| pingu_V3 | mint=FILE |
MINT flat file | None |
| pingu_V3 | pairwise=FILE |
Load interaction data from existing Pingu Pairwise file | None |
| pingu_V3 | pfamdata=FILE |
Delimited files containing domain organisation of sequences | None |
| pingu_V3 | pingupickle=FILE |
Full path to Pingu pickle file to look for/use/save | pingu.pickle |
| pingu_V3 | qslimfinder=FILE |
File containing sequences matching Sample names for Query SLiMFinder runs | None |
| pingu_V3 | reactome=FILE |
Reactome interactions flat file | None |
| pingu_V3 | screenddi=FILE |
Whether to screen out probably domain-domain interactions from file | None |
| pingu_V4 | biogrid=FILE |
BioGRID flat file | None |
| pingu_V4 | dip=FILE |
DIP interactions flat file | None |
| pingu_V4 | domino=FILE |
Domino interactions flat file | None |
| pingu_V4 | evidence=FILE |
Mapping file for evidence terms | None |
| pingu_V4 | intact=FILE |
IntAct flat file | None |
| pingu_V4 | mint=FILE |
MINT flat file | None |
| pingu_V4 | ppiout=FILE |
Save pairwise PPI file following processing (if rest=None) | None |
| pingu_V4 | queryppi=FILE |
Load a file of 'Query','Hub' PPI and generate expanded PPI Datasets in PPI.*/ | None |
| pingu_V4 | queryseq=FILE |
Fasta file containing the Query protein sequences corresponding to QuerySeq | *.fas |
| pingu_V4 | reactome=FILE |
Reactome interactions flat file | None |
| presto_V5 | aaprop=FILE |
Amino Acid property matrix file. | aaprop.txt |
| presto_V5 | domfilter=FILE |
Use the DomFilter options, reading domains from FILE | None |
| presto_V5 | motifout=FILE |
Filename for output of reformatted (and filtered?) motifs in PRESTO format | None |
| presto_V5 | motifs=FILE |
File of input motifs/peptides | None |
| presto_V5 | posmatrix=FILE |
Score matrix for amino acid combinations used in pos weighting. (conscore=pos builds from propmatrix) | None |
| presto_V5 | searchdb=FILE |
Protein Fasta file to search (or second motif file to compare) | None |
| prodigis | peptides=FILE |
File containing list of identified peptides | None |
| prodigis | positives=FILE |
File of positively identified proteins matching peptide lists | None |
| prodigis | source=FILE |
File containing source protein data (including UniProt AccNum column) | None |
| qslimfinder | aadimerfreq=FILE |
Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) (!!!Experimental!!!) | None |
| qslimfinder | aafreq=FILE |
Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) | None |
| qslimfinder | addquery=FILE |
Adds query sequence(s) to batch jobs from FILE | None |
| qslimfinder | altdis=FILE |
Alternative all by all distance matrix for relationships | None |
| qslimfinder | focus=FILE |
FILE containing focal groups for SLiM return (see Manual for details) | None |
| qslimfinder | gablamdis=FILE |
Alternative GABLAM results file | None |
| qslimfinder | megaslim=FILE |
Make/use precomputed results for a proteome (FILE) in fasta format | None |
| qslimfinder | negatives=FILE |
Multiply raw probabilities by under-representation in FILE (!!!Experimental!!!) | None |
| qslimfinder | resfile=FILE |
Main QSLiMFinder results table | qslimfinder.csv |
| qslimfinder | seqin=FILE |
Sequence file to search | None |
| qslimfinder | slimcheck=FILE |
Motif file/list to add to resfile output | |
| qslimfinder_V1.9 | aadimerfreq=FILE |
Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) (!!!Experimental!!!) | None |
| qslimfinder_V1.9 | aafreq=FILE |
Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) | None |
| qslimfinder_V1.9 | addquery=FILE |
Adds query sequence(s) to batch jobs from FILE | None |
| qslimfinder_V1.9 | altdis=FILE |
Alternative all by all distance matrix for relationships | None |
| qslimfinder_V1.9 | focus=FILE |
FILE containing focal groups for SLiM return (see Manual for details) | None |
| qslimfinder_V1.9 | gablamdis=FILE |
Alternative GABLAM results file | None |
| qslimfinder_V1.9 | negatives=FILE |
Multiply raw probabilities by under-representation in FILE (!!!Experimental!!!) | None |
| qslimfinder_V1.9 | resfile=FILE |
Main QSLiMFinder results table | qslimfinder.csv |
| qslimfinder_V1.9 | seqin=FILE |
Sequence file to search | None |
| qslimfinder_V1.9 | slimcheck=FILE |
Motif file/list to add to resfile output | |
| revert | aliasfile=FILE |
Delimited file of 'Name','Alias' to use in place of batch summary files | *.alias.tdt |
| revert | basefile=FILE |
Root of output files. Defaults to `virusgb.genome` if blank/None | None |
| revert | genome=FILE |
Fasta file containing contigs or chromosomes of host genome | genome.fas |
| revert | searchdb=FILE |
Fasta file of viral (& host?) proteins for assembly annotation. Use viral proteins if None. | |
| rje | errorlog=FILE |
If given, will write errors to an additional error file. | None |
| rje | log=FILE |
Redirect log to FILE | Default = calling_program.log |
| rje_1433 | litfile=FILE |
File of literature interactions | 1433_Lit.tdt |
| rje_1433 | msfile=FILE |
File containing MS Data | 1433_msdata_full.txt |
| rje_aaprop | aaprop=FILE |
Amino Acid property matrix file. | aaprop.txt |
| rje_aic | biomart=FILE |
File containing BioMart download | |
| rje_aic | pridefile=FILE |
Delimited file containing PRIDE IDs and Protein IDs | |
| rje_aic | refseq=FILE |
File containing RefSeq download in GenBank format | |
| rje_archive | archived=FILE |
File to output archive summaries into | 'BASEFILE.archived.tdt' |
| rje_archive | backupdb=FILE |
File to output backup summaries into | 'BASEFILE.backups.tdt' |
| rje_archive | basefile=FILE |
This will set the 'root' filename for output files (FILE.*), including the log | 'rds' |
| rje_archive | dormant=FILE |
File to output dormant directories into | 'BASEFILE.dormant.tdt' |
| rje_archive | projects=FILE |
Delimited file of `Project` and `RDS` code. If provided, will not use rds=X | 'projects.tdt' |
| rje_biogrid | genecards=FILE |
File of links between IDs. For human, should have HGNC and EnsLoci columns. | None |
| rje_biogrid | ppifile=FILE |
PPI database flat file | None |
| rje_biogrid | seqin=FILE |
Sequence file containing protein sequences with appropriate Accession Numbers/IDs | None |
| rje_blast | blastd=FILE |
BLAST database (BLAST -d FILE) | None |
| rje_blast | blasti=FILE |
Input file (BLAST -i FILE) | None |
| rje_blast | blasto=FILE |
Output file (BLAST -o FILE) | *.blast |
| rje_blast | blastopt=FILE |
File containing raw BLAST options (applied after all others) | |
| rje_blast_V1 | blastd=FILE |
BLAST database (BLAST -d FILE) | None |
| rje_blast_V1 | blasti=FILE |
Input file (BLAST -i FILE) | None |
| rje_blast_V1 | blasto=FILE |
Output file (BLAST -o FILE) | *.blast |
| rje_blast_V1 | blastopt=FILE |
File containing raw BLAST options (applied after all others) | |
| rje_blast_V2 | blastd=FILE |
BLAST database (BLAST -d FILE) | None |
| rje_blast_V2 | blasti=FILE |
Input file (BLAST -i FILE) | None |
| rje_blast_V2 | blasto=FILE |
Output file (BLAST -o FILE) | *.blast |
| rje_blast_V2 | blastopt=FILE |
File containing raw BLAST options (applied after all others) | |
| rje_dbase | makedb=FILE |
Makes a database from combined databases | None |
| rje_dbase | taxadb=FILE |
File containing details of taxanomic sub-databases to make | None |
| rje_dismatrix_V2 | loadmatrix=FILE |
Loads a matrix from FILE | None |
| rje_dismatrix_V3 | loadmatrix=FILE |
Loads a matrix from FILE | None |
| rje_embl | datout=FILE |
Name of new (reduced) DAT file of extracted sequences | None |
| rje_embl | dbindex=FILE |
Database index file | uniprot.index |
| rje_embl | embldat=FILE |
Name of EMBL file | None |
| rje_embl | ftout=FILE |
Outputs table of features into FILE | None |
| rje_embl | linkout=FILE |
Table of extracted Database links | None |
| rje_embl | tabout=FILE |
Table of extracted details | None |
| rje_ensembl | datpickup=FILE |
Text file containing names of proteins already processed (skip and append) | ensdat.txt |
| rje_ensembl | goids=FILE |
File containing GO IDs | GO.terms_ids_obs |
| rje_ensembl | hgncmap=FILE |
File to be used for HGNC ID mapping | |
| rje_ensembl | pfam=FILE |
Path to PFam LS file | /home/richard/Databases/PFam/Pfam_ls |
| rje_ensembl | signalp=FILE |
Path to SIGNALP program | /home/richard/Bioware/signalp-3.0/signalp |
| rje_ensembl | tmhmm=FILE |
Path to TMHMM program | /home/richard/Bioware/TMHMM2.0c/bin/tmhmm |
| rje_ensembl | unispec=FILE |
Alternative UniProt species file | None |
| rje_genbank | basefile=FILE |
Root of output file names (same as input file by default) | |
| rje_genbank | seqin=FILE |
Input Genbank file | |
| rje_genecards | cardout=FILE |
File for output of genecard data | genecards.tdt |
| rje_genecards | ensloci=FILE |
File of EnsLoci genome to incorporate | /home/richard/Databases/EnsEMBL/ens_HUMAN.loci.fas |
| rje_genecards | hgncdata=FILE |
HGNC download file containing data | |
| rje_genemap | aliases=FILE |
Files containing aliases only. | |
| rje_genemap | ensloci=FILE |
File of EnsLoci genome to incorporate | None |
| rje_genemap | genepickle=FILE |
Use pickle of GeneMap data without additional loading/processing etc. | None |
| rje_genemap | hgncdata=FILE |
Download file containing HGNC data. | |
| rje_genemap | mgidata=FILE |
Download file containing MGI data (ftp://ftp.informatics.jax.org/pub/reports/MGI_MouseHumanSequence.rpt) | |
| rje_genemap | pfamdata=FILE |
Delimited files containing domain organisation of sequences | None |
| rje_genemap | pickledata=FILE |
Genemap pickle to import and use. | |
| rje_genemap | sourcedata=FILE |
File containing data in order of preference regarding conflicting data. | |
| rje_genomics | tdtfile=FILE |
Input delimited text file with data to convert | None |
| rje_glossary | infile=FILE |
Input file of Term:Definition | glossary.tdt |
| rje_glossary | outfile=FILE |
Output file name (input.html by default) | |
| rje_go | obofile=FILE |
Input GO OBO V1.2 download | None |
| rje_hivqsf | genemap=FILE |
Delimited human gene mapping data | |
| rje_hivqsf | hhpid=FILE |
Delimited text file containing HHPID interactions | |
| rje_hivqsf | hivseq=FILE |
File containing HIV sequences | |
| rje_hm_html | titletext=FILE |
File containing (Page,ID,Title) | titletext.tdt |
| rje_hmm_V1 | hmmout=FILE |
Pipe results of HMM searches into FILE | None |
| rje_hmm_V1 | hmmtab=FILE |
Delimited table of results ('None' to skip) | searchdb.tdt |
| rje_hmm_V1 | searchdb=FILE |
Fasta file to search with HMMs | None |
| rje_hmm_V2 | hmmout=FILE |
Pipe results of HMM searches into FILE | None |
| rje_hmm_V2 | hmmtab=FILE |
Delimited table of results ('None' to skip) | searchdb.tdt |
| rje_hmm_V2 | searchdb=FILE |
Fasta file to search with HMMs | None |
| rje_hpc | jobini=FILE |
Ini file to pass to the called program | None |
| rje_hpc | seqin=FILE |
Input sequence file to farm out | None |
| rje_html | tabber=FILE |
Tabber javascript file location | 'tabber.js' |
| rje_iridis | iini=FILE |
Ini file to pass to the called program | None |
| rje_iridis | resfile=FILE |
Main output file for iX run | islimfinder.csv |
| rje_iridis | resfile=FILE |
Main output file for iX run | islimfinder.csv |
| rje_iridis | resfile=FILE |
Main output file for iX run | islimfinder.csv |
| rje_iridis | seqin=FILE |
Input sequence file to farm out | None |
| rje_markov | aafreq=FILE |
Generate expected 1mer frequencies from FILE of aafreq | None |
| rje_markov | seqin=FILE |
File with input sequences | None |
| rje_markov | xmerfile=FILE |
File from which to load Xmer counts and build suffix tree | None |
| rje_mascot | mascot=FILE |
Name of MASCOT csv file | None |
| rje_mirna | arraydata=FILE |
File of array data for Cleal analysis | |
| rje_mirna | miranda=FILE |
Miranda prediction file | |
| rje_mirna | seqin=FILE |
Main file for analysis, containing UTRs | |
| rje_mirna | validated=FILE |
Validate mRNA target file | |
| rje_misc | infile=FILE |
Name of input file for relevant task | None |
| rje_mitab | mitab=FILE |
MITAB interaction file | |
| rje_motiflist | aaprop=FILE |
Amino Acid property matrix file. | aaprop.txt |
| rje_motiflist | domfilter=FILE |
Use the DomFilter options, reading domains from FILE | None |
| rje_motiflist | motifs=FILE |
File of input motifs/peptides | None |
| rje_motiflist | posmatrix=FILE |
Score matrix for amino acid combinations used in pos weighting. (conscore=pos builds from propmatrix) | None |
| rje_mysql | buildfile=FILE |
Output file for MySQL Build statements | mysql_build.txt |
| rje_mysql | sqldump=FILE |
Read in an SQL dump file and convert into CSV | None |
| rje_obj | errorlog=FILE |
If given, will write errors to an additional error file. | None |
| rje_obj | log=FILE |
Redirect log to FILE | Default = calling_program.log |
| rje_omim | omim=FILE |
Input file (OMIM text download) | 'omim.txt' |
| rje_pacbio | seqin=FILE |
Subread sequence file for analysis | None |
| rje_pam | altpam=FILE |
Alternative to PAM file input = matrix needing scaling by aafreq | None |
| rje_pam | pamout=FILE |
Name for rescaled PAM matrix output | *.pam named after altpam=FILE |
| rje_pam | seqin=FILE |
Sequence file from which to calculate AA freq for scaling | None |
| rje_paml | ctlfile=FILE |
PAML control file to use | 'codeml.ctl' |
| rje_paml | infile=FILE |
Name for PAML sequence input file | 'infile' |
| rje_paml | outfile=FILE |
Name of PAML output file | 'mlc' |
| rje_pattern_discovery | batchout=FILE |
Create a batch file containing individual seqin=FILE calls. | None |
| rje_pattern_discovery | info=FILE |
Calculate information content of motifs in FILE (based on AA Freq from seqin, if given) | None |
| rje_pattern_discovery | outfile=FILE |
Output file name | seqin.teiresias.* |
| rje_pattern_discovery | seqin=FILE |
Sequence File to search | None |
| rje_phos | pelm=FILE |
Filename for phosphoELM download | None |
| rje_phos | pelmfas=FILE |
Filename for fasta file output of pELM sequences | pelm.fas |
| rje_phos | phosblast=FILE |
Fasta file of sequences to perform phosBLAST method against pELM | None |
| rje_phos | phosres=FILE |
Delimited text file containing input sequence, position and evidence | *.phosres.tdt |
| rje_ppi | pairwise=FILE |
Input PPI pairwise file, containing Hub, Spoke and optional Evidence columns | |
| rje_price | resfile=FILE |
Results file | price.tdt |
| rje_price | seqin=FILE |
Input sequence alignment in fasta format (over-rides batch=LIST) | None |
| rje_samtools | altcontrol=FILE |
MPileup or processed TDT file to be used for control SNP frequencies in Alt genome | |
| rje_samtools | alttreatment=FILE |
MPileup or processed TDT file to be used for treatment SNP frequencies in Alt genome | |
| rje_samtools | control=FILE |
MPileup or processed TDT file to be used for control SNP frequencies | |
| rje_samtools | readcheck=FILE |
SAM/Pileup/RID file with read mappings | None |
| rje_samtools | snptable=FILE |
Table of SNPs of cross-reference with FDR SNP output | |
| rje_samtools | treatment=FILE |
MPileup or processed TDT file to be used for treatment SNP frequencies | |
| rje_samtools_V0 | mutpileup=FILE |
MPileup results for mutant genome resequencing | None |
| rje_samtools_V0 | wtpileup=FILE |
MPileup results for wildtype genome resequencing | None |
| rje_scansite | outfile=FILE |
Output file name | scansite.tdt |
| rje_seq | fasdb=FILE |
Fasta format database to extract sequences from | None |
| rje_seq | filterout=FILE |
Saves filtered sequences (as fasta) into FILE. *NOTE: File is appended if append=T* | None |
| rje_seq | haqbat=FILE |
Generate a batch file (FILE) to run HAQESAC on generated BLAST files, with seqin as queries | None |
| rje_seq | mapdna=FILE |
Map DNA sequences from FILE onto sequences of same name in protein alignment | None |
| rje_seq | mapseq=FILE |
Maps sequences from FILE to sequences of same name | None |
| rje_seq | relcons=FILE |
Returns a file containing Pos AbsCons RelCons | None |
| rje_seq | seqin=FILE |
Loads sequences from FILE (fasta,phylip,aln,uniprot or fastacmd names from fasdb) | None |
| rje_seq | seqout=FILE |
Saves 'tidied' sequences to FILE after loading and manipulations | None |
| rje_seqgen | aafreq=FILE |
File from which to read AA Freqs | None |
| rje_seqgen | outfile=FILE |
Output delimited file of scrambled peptides or peptide and scrambled sequence. | scramble.tdt |
| rje_seqgen | screenfile=FILE |
File of Xmers to screen in generated sequences | None |
| rje_seqgen | seqin=FILE |
Input sequence file to randomise | None |
| rje_seqgen | xmerfile=FILE |
File from which to read Xmer frequencies for sequence generation | None |
| rje_seqgen | xmerseq=FILE |
Sequence file from which to calculate Xmer frequencies | None |
| rje_seqlist | seqdb=FILE |
Sequence file from which to extract sequences (fastacmd/index formats) | None |
| rje_seqlist | seqin=FILE |
Sequence input file name. | None |
| rje_seqlist | seqout=FILE |
Whether to output sequences to new file after loading and filtering | None |
| rje_seqplot | occfile=FILE |
File containing motif occurrences to plot | None |
| rje_seqplot | seqin=FILE |
File containing input sequences | None |
| rje_slimcalc | aaprop=FILE |
Amino Acid property matrix file. | aaprop.txt |
| rje_slimcalc | orthdb=FILE |
File to use as source of orthologues for GOPHER | |
| rje_slimcalc | posmatrix=FILE |
Score matrix for amino acid combinations used in pos weighting. (conscore=pos builds from propmatrix) | None |
| rje_slimcalc | vnematrix=FILE |
BLOSUM matrix file to use for VNE relative conservation | |
| rje_slimcore | aafreq=FILE |
Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) | None |
| rje_slimcore | altdis=FILE |
Alternative all by all distance matrix for relationships | None |
| rje_slimcore | domtable=FILE |
Domain table containing domain ("Type") and sequence ("Name") pairings for additional UPC | None |
| rje_slimcore | equivout=FILE |
File for equivalence list output | equiv.txt |
| rje_slimcore | gablamdis=FILE |
Alternative GABLAM results file | None |
| rje_slimcore | megaslim=FILE |
Make/use precomputed results for a proteome (FILE) in fasta format | None |
| rje_slimcore | randsource=FILE |
Source for new sequences for random datasets (replaces UPCs) | None |
| rje_slimcore | seqin=FILE |
Sequence file to search. Over-rules batch mode (and uniprotid=LIST). | None |
| rje_slimfungo | gomap=FILE |
Mapping of sequences to GO categories | None |
| rje_slimfungo | obofile=FILE |
Input GO OBO V1.2 download | None |
| rje_slimfungo | occdata=FILE |
File of motif occurrences. Must have | None |
| rje_slimfungo | seqin=FILE |
File of input sequences | None |
| rje_slimhtml | slimdesc=FILE |
File containing descriptions for SLiMs | slimdesc.txt |
| rje_slimhtml | titletext=FILE |
File containing (Page,ID,Title) | titletext.tdt |
| rje_slimlist | motifout=FILE |
Name of output file for reformatted/filtered SLiMs (PRESTO format) | None |
| rje_slimlist | motifs=FILE |
File of input motifs/peptides | None |
| rje_slimlist | motinfo=FILE |
Filename for output of motif summary table (if desired) | None |
| rje_spf | infile=FILE |
The input SPF file | input.spf |
| rje_spf | log=FILE |
The name of the output log (*.log) | rje_spf.log |
| rje_synteny | basefile=FILE |
Basename for output files | ftgablam basefile |
| rje_synteny | ftfile=FILE |
File of reference genome features | *.Feature.tdt |
| rje_synteny | ftgablam=FILE |
GABLAM search results (e.g. from PAGSAT) of Genes/Proteins against assembly regions | None |
| rje_synteny | refgenome=FILE |
Fasta/Genbank file of reference genome for assessment (also *.gb for full functionality) | None |
| rje_taxamap | protdesc=FILE |
Delimited file of protein, description | None |
| rje_taxonomy | namemap=FILE |
NCBI Name mapping file | names.dmp |
| rje_taxonomy | specfile=FILE |
Uniprot species code download. | speclist.txt |
| rje_taxonomy | taxmap=FILE |
NCBI Node Dump File | nodes.dmp |
| rje_tm | seqin=FILE |
Sequence file for which predictions have been made | None |
| rje_tm | signalp=FILE |
SignalP output file | None |
| rje_tm | tmhmm=FILE |
TMHMM output file | None |
| rje_tree | cwtree=FILE |
Make a ClustalW NJ Tree from FILE (will save *.ph or *.phb) | None |
| rje_tree | disin=FILE |
load distance matrix from FILE (Phylip format for use with distance matrix methods) | None |
| rje_tree | phyoptions=FILE |
File containing extra Phylip tree-making options ('batch running') to use | None |
| rje_tree | protdist=FILE |
File containing extra Phylip PROTDIST options ('batch running') to use | None |
| rje_tree | savetree=FILE |
Save a generated tree as FILE | seqin.maketree.nsf |
| rje_uniprot | acctable=FILE |
Delimited text file from which to retrieve a list of accession numbers | None |
| rje_uniprot | dbindex=FILE |
Database index file | uniprot.index |
| rje_uniprot | uniprot=FILE |
Name of UniProt file | None |
| rje_xml | parse=FILE |
Source file for reading XML file | None |
| rje_xref | filexref=FILE |
File to XRef and expand with xrefs before re-saving | |
| rje_yeast | pillars=FILE |
YGOB pillars file | Pillars.tab |
| rje_yeast | ppifile=FILE |
Input PPI data (two columns of binary interactors) | Y2H_union.txt |
| rje_yeast | seqin=FILE |
Input sequence file containing yeast sequences | Proteins.fas |
| rje_yeast | xref=FILE |
Yeast identifier XRef file (e.g. BioMart download) | yeast_xref.20101222.tdt |
| samphaser | basefile=FILE |
Root of output file names (same as Pileup input file by default) | |
| samphaser | pileup=FILE |
Pileup file of reads against input genome. | |
| scap | scapback=FILE |
File with sequences for background SCAP calculations | None |
| scap | seqin=FILE |
File with input sequences for testing | None |
| scap | xmerback=FILE |
File with sequences for background Markov Chain calculations (can be pickle) | seqin |
| seqforker | log=FILE |
Redirect log to FILE | Default = calling_program.log |
| seqforker | seqin=FILE |
Input sequence file | None |
| seqmapper | basefile=FILE |
Set resfile=FILE and log=FILE at the same time | |
| seqmapper | mapdb=FILE |
File of sequences to map sequences onto | None |
| seqmapper | resfile=FILE |
Base of output filenames (*.mapped.fas, *.missing.fas & *.mapping.tdt) | seqin.mapdb |
| seqmapper | seqin=FILE |
File of sequences to be mapped | None |
| sfmap2png | seqin=FILE |
*.mapping.fas file to use as input data | |
| slim_pickings | datout=FILE |
Extract UniProt entries from parent proteins where possible into FILE | uniprot_extract.dat |
| slim_pickings | ftout=FILE |
Make a file of UniProt features for extracted parent proteins, where possible, incoroprating SLIMs | None |
| slim_pickings | occres=FILE |
Output individual occurrence data in FILE | None |
| slim_pickings | outfile=FILE |
Name of output file. | slimdisc_results.csv |
| slimbench | compdb=FILE |
Motif file to be used for benchmarking | elmclass file |
| slimbench | elmclass=FILE |
Download from ELM website of ELM classes | elm_classes.tsv |
| slimbench | elmdat=FILE |
File of downloaded UniProt entries (See rje_uniprot for more details) | 'ELM.dat' |
| slimbench | elmdomains=FILE |
Download from ELM website of ELM Pfam domain interactors | elm_interaction_domains.tsv |
| slimbench | elminstance=FILE |
Download from ELM website of ELM instances | elm_instances.tsv |
| slimbench | elminteractors=FILE |
Download from ELM website of ELM interactors | elm_interactions.tsv |
| slimbench | occbenchpos=FILE |
File of all positive occurrences for OccBench | genpath/ELM_OccBench/ELM.full.ratings.csv |
| slimbench | randsource=FILE |
Source for random/simulated dataset sequences. If species, will extract from UniProt | HUMAN |
| slimbench | searchini=FILE |
INI file containing SLiMProb search options that restrict returned positives | |
| slimbench_V1 | compdb=FILE |
Motif file to be used for benchmarking (default = reduced elmclass file) | |
| slimbench_V1 | dmidata=FILE |
File of 3DID DMI data | '3did.DMI.csv' |
| slimbench_V1 | elmclass=FILE |
Download from ELM website of ELM classes | 'elm_classes.tsv' |
| slimbench_V1 | elminstance=FILE |
Download from ELM website of ELM instances | 'elm_instances.tsv' |
| slimbench_V1 | elmpfam=FILE |
Download from ELM website of ELM Pfam domain interactors | 'elm_interaction_domains.tsv' |
| slimbench_V1 | pdbdata=FILE |
File mapping PDB identifiers onto genes/proteins | |
| slimbench_V1 | pfamdata=FILE |
File mapping PFam domains onto genes/proteins (BioMart or HMM search) | |
| slimbench_V1 | randsource=FILE |
Source for new sequences for random datasets | None |
| slimbench_V1 | uniprot=FILE |
File of downloaded UniProt entries (See rje_uniprot for more details) | 'ELM.dat' |
| slimbench_V1 | xrefdata=FILE |
File of gene identifier cross-reference data from rje_genemap | |
| slimdip | basefile=FILE |
Sets the basefile for all input/output. If not given, will use the ppifile=FILE base | None |
| slimdip | motifs=FILE |
File containing the SLiMs to analyse. (Required.) "ELM" will create/use ELM download. | ELM |
| slimfarmer | jobini=FILE |
Ini file to pass to the farmed SLiMSuite run. (Also used for SLiMFarmer options if qsub=T.) | None |
| slimfarmer | resfile=FILE |
Main output file for SLiMSuite run | `farm`.csv |
| slimfarmer | seqin=FILE |
Input sequence file to farm out | None |
| slimfinder | aadimerfreq=FILE |
Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) (!!!Experimental!!!) | None |
| slimfinder | focus=FILE |
FILE containing focal groups for SLiM return (see Manual for details) | None |
| slimfinder | gablamdis=FILE |
Alternative GABLAM results file | None |
| slimfinder | megaslim=FILE |
Make/use precomputed results for a proteome (FILE) in fasta format | None |
| slimfinder | resfile=FILE |
Main SLiMFinder results table | slimfinder.csv |
| slimfinder_V4.9 | aadimerfreq=FILE |
Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) (!!!Experimental!!!) | None |
| slimfinder_V4.9 | aafreq=FILE |
Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) | None |
| slimfinder_V4.9 | altdis=FILE |
Alternative all by all distance matrix for relationships | None |
| slimfinder_V4.9 | focus=FILE |
FILE containing focal groups for SLiM return (see Manual for details) | None |
| slimfinder_V4.9 | gablamdis=FILE |
Alternative GABLAM results file | None |
| slimfinder_V4.9 | negatives=FILE |
Multiply raw probabilities by under-representation in FILE (!!!Experimental!!!) | None |
| slimfinder_V4.9 | resfile=FILE |
Main SLiMFinder results table | slimfinder.csv |
| slimfinder_V4.9 | seqin=FILE |
Sequence file to search | None |
| slimfinder_V4.9 | slimcheck=FILE |
Motif file/list to add to resfile output | |
| slimfrap | domtable=FILE |
Table of domain predictions | None |
| slimfrap | elm=FILE |
File of ELM Motifs | None |
| slimfrap | nandr=FILE |
File of Neduva & Russell motifs | None |
| slimfrap | pairwise=FILE |
Pingu Pairwise PPI file | None |
| slimfrap | pickledata=FILE |
Genemap pickle to import and use. (See other rje_genemap options) | None |
| slimgoer | resfile=FILE |
Basefile for SLiMSearch results CSV files | |
| slimjim | pairwise=FILE |
Pingu Pairwise output file | |
| slimjim | resfile=FILE |
Main SLiMFinder results file | |
| slimjim | singlesf=FILE |
Path to *.slimdb file for which to generate graphics for single run | |
| slimmutant | dmifile=FILE |
Delimited text file containing domain-motif interaction data | 'elm_interaction_domains.tsv' |
| slimmutant | motifs=FILE |
Input file of SLiMs | |
| slimmutant | mutfile=FILE |
Delimited text file with sequence mutation info. Sets basefile. | |
| slimmutant | resfile=FILE |
Main SLiMProb results table (*.csv and *.occ.csv) | slimprob.csv |
| slimmutant | seqin=FILE |
Input file with protein sequences | |
| slimparser | restin=FILE |
Full REST output file, REST jobid (number), or full REST call URL (http://...) | |
| slimpid | ddi=FILE |
iPFam domain-domain interaction file | |
| slimpid | fam=FILE |
File of GABLAM results for family-based methods | |
| slimpid | ppi=FILE |
Pingu PPI File with Gene, EnsLoci & PPI headers | |
| slimprob | aadimerfreq=FILE |
Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) | None |
| slimprob | aafreq=FILE |
Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) | None |
| slimprob | altdis=FILE |
Alternative all by all distance matrix for relationships | None |
| slimprob | background=FILE |
Use observed support in background file for over-representation calculations | None |
| slimprob | gablamdis=FILE |
Alternative GABLAM results file | None |
| slimprob | megaslim=FILE |
Make/use precomputed results for a proteome (FILE) in fasta format | None |
| slimprob | motifs=FILE |
File of input motifs/peptides (also motif=X) | None |
| slimprob | negatives=FILE |
Multiply raw probabilities by under-representation in FILE | None |
| slimprob | resfile=FILE |
Main SLiMProb results table (*.csv and *.occ.csv) | slimprob.csv |
| slimprob_V1.4 | aadimerfreq=FILE |
Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) | None |
| slimprob_V1.4 | aafreq=FILE |
Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) | None |
| slimprob_V1.4 | altdis=FILE |
Alternative all by all distance matrix for relationships | None |
| slimprob_V1.4 | background=FILE |
Use observed support in background file for over-representation calculations | None |
| slimprob_V1.4 | gablamdis=FILE |
Alternative GABLAM results file | None |
| slimprob_V1.4 | motifs=FILE |
File of input motifs/peptides | None |
| slimprob_V1.4 | negatives=FILE |
Multiply raw probabilities by under-representation in FILE | None |
| slimprob_V1.4 | resfile=FILE |
Main SLiMProb results table (*.csv and *.occ.csv) | slimprob.csv |
| slimprob_V1.4 | seqin=FILE |
Sequence file to search | None |
| slimsearch | aadimerfreq=FILE |
Use empirical dimer frequencies from FILE (fasta or *.aadimer.tdt) | None |
| slimsearch | aafreq=FILE |
Use FILE to replace individual sequence AAFreqs (FILE can be sequences or aafreq) | None |
| slimsearch | altdis=FILE |
Alternative all by all distance matrix for relationships | None |
| slimsearch | background=FILE |
Use observed support in background file for over-representation calculations | None |
| slimsearch | gablamdis=FILE |
Alternative GABLAM results file | None |
| slimsearch | motifs=FILE |
File of input motifs/peptides | None |
| slimsearch | negatives=FILE |
Multiply raw probabilities by under-representation in FILE | None |
| slimsearch | resfile=FILE |
Main SLiMSearch results table | slimsearch.csv |
| slimsearch | seqin=FILE |
Sequence file to search | None |
| smrtscape | basefile=FILE |
Sets the root filename for all output, including the log | smrtscape |
| smrtscape | preassembly=FILE |
Preassembly fasta file for which to assess/correct over-fragmentation | None |
| smrtscape | seqin=FILE |
Subread sequence file for analysis (over-rides batch command) | None |
| smrtscape_V1 | preassembly=FILE |
Preassembly fasta file to assess/correct over-fragmentation (use seqin=FILE for subreads) | None |
| smrtscape_V1 | seqin=FILE |
Subread sequence file for analysis | None |
| snapper | basefile=FILE |
Root of output file names (same as SNP input file by default) | |
| snapper | ftfile=FILE |
Input feature file (locus,feature,position,start,end) | *.Feature.tdt |
| snapper | reference=FILE |
Fasta (with accession numbers matching Locus IDs) or genbank file of reference genome. | |
| snapper | snpmap=FILE |
Input table of SNPs for standalone mapping and output (should have locus and pos info) | None |
| snp_mapper | basefile=FILE |
Root of output file names (same as SNP input file by default) | |
| snp_mapper | ftfile=FILE |
Input feature file (locus,feature,position,start,end) | *.Feature.tdt |
| snp_mapper | genbase=FILE |
Basefile for Genbank output. Will use base of seqin if None | |
| snp_mapper | seqin=FILE |
Sequence input file with accession numbers matching Locus IDs, or Genbank file. | |
| snp_mapper | snpfile=FILE |
Input table of SNPs to map and output (should have locus and pos info, see above) | |
| trex | basefile=FILE |
Root of output file names | preassembly basefile |
| unifake | aliases=FILE |
File of aliases to be added to Accession number list (for indexing) | None |
| unifake | datout=FILE |
Name of output DAT file | Default input FILE.dat |
| unifake | pfam=FILE |
PFam HMM download | None |
| unifake | seqin=FILE |
Input sequence file. See rje_seq documentation for filtering options. | None |
| unifake | signalp=FILE |
Path to SignalP program | None |
| unifake | tmhmm=FILE |
Path to TMHMM program | None |
| wormpump | outfile=FILE |
Name of output file | wormpump.tdt |
© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.