2 Virtual Iron 2 Big Iron Commod ity Iron Algorith ms: Big
Small Data: Big Small Plant Biologists Community Computational
Biologists iPlant Cyberinfrastructure High-Level View of iPlant
CI
Slide 3
What we need How to download the tool or source code, including
installation and usage instructions. The required version of the
program. A sample dataset and the expected results to be output.
The set of parameters and command line switches that match the
expected execution of the tool. A brief text description of the
tool, written for someone who has not used the tool before. This
should include links to literature for further reading.
Slide 4
Slide 5
5 A few things to keep in mind iPlants resources are limited
iPlant cannot generate new data iPlant needs collaborators with
expertise Complex data integration and interactive visualization
are big problems 5 Biology and Computer Science have technical
jargon: Clear communication and patience are essential!
What? Name: Tool name Description: What the tool does Type:
"executable" (more will come) [location]: Where the executable
reside (we'll tell you that) Attribution: Who wrote it Version:
Which version (we want to get the right thing)
Slide 12 cat d infile >outfile"> command [options]
infiles outfiles { "name": "cat", "description": "Reads the
contents of a file and writes it to standard output", "type":
"executa">
> command [options] infiles outfiles { "name": "cat",
"description": "Reads the contents of a file and writes it to
standard output", "type": "executable", "location": "/bin/cat",
"attribution": "A really smart UNIX guru like Rob Pike wrote the
original version. A cat utility appeared in Version 1 AT&T
UNIX. Dennis Ritchie designed and wrote the first man page.",
"version": "7.4.1", } > cat d infile >outfile
Slide 15 cat b filename.txt >out.txt From the metadata
description"> cat b filename.txt >out.txt From the metadata
description"> cat b filename.txt >out.txt From the metadata
description" title="{ "id":"", "name": "Linux cat", "type": "cat",
"input":[], "groups":[] "output":[] } >cat b filename.txt
>out.txt From the metadata description">
{ "id":"", "name": "Linux cat", "type": "cat", "input":[],
"groups":[] "output":[] } >cat b filename.txt >out.txt From
the metadata description
Slide 16 cat b fi"> cat b filename.txt >out.txt"> cat
b fi" title="{ "input":[ { "id":"catin", "name":"File to read:",
"type":"File", "multiplicity":"single", "order":2 }, ], "groups":
[], "output":[] } >cat b fi">
{ "input":[ { "id":"catin", "name":"File to read:",
"type":"File", "multiplicity":"single", "order":2 }, ], "groups":
[], "output":[] } >cat b filename.txt >out.txt
Single site Tool Metadata { "location" : "/usr/bin/Rscript",
"name" : "singleSite", "type" : "executable", "version" : 1.0,
"description" : "Single Site analysis for breeding platform",
"attribution" : "Graham McLaren ([email protected])" }
Slide 22
singleSite.R data_1cat b filename.txt | grep cat -b grep
Filename.txt">
>cat b filename.txt | grep cat -b grep Filename.txt
Slide 36
{ "analysis_id":"", "analysis_name":"File Read and Display",
"type":"Concatenate and print a file", "description":"Reads a file
and prints to standard output", "steps":[ { "name":"cat",
"description":"Reads a file and prints to standard output",
"template_id":"", "config":{ } }, { "name":"grep_search",
"description":"Searches within a file for supplied text",
"template_id":"", "config":{ } }, ]