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Juntian Wei BCO submission.md #176

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Juntian Wei BCO submission.md #176

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355 changes: 355 additions & 0 deletions Juntian Wei BCO final draft.json
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{
"bco_id": "http://biocomputeobject.org/BCO_000549",
"checksum": "0113397a5cdc2e40b6221d69cd6a7452c20b8266af2917d7a0a2442f714c760f",
"bco_spec_version": "1.3.0",
"provenance_domain": {
"name": "iMir: An integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq",
"version": "1.0.0",
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good job fixing version.

"license": "https://spdx.org/licenses/CC-BY-4.0.html",
"created": "2019-10-16T18:59:23.577045",
"modified": "2019-10-08T21:40:44.475711",
"review": [
{
"status": "in-review",
"reviewer_comment": "Reviewed by BioCompute technical assistant, approval pending modification by author",
"reviewer": {
"orcid": "https://orcid.org/0000-0002-8824-4637",
"affiliation": "George Washington University",
"contribution": [
"createdBy"
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Incorrect contribution type. Please modify. See #148

],
"name": "Janisha Patel",
"email": "janishapatel@gwu.edu"
},
"date": "10_16_2019"
}
],
"contributors": [
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Why are the publication authors not added as contributors? See #113

{
"name": "",
"orcid": "",
"affiliation": "",
"contribution": [
"createdBy"
],
"email": "jwei48@gwmail.gwu.edu"
Comment on lines +27 to +35
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Why is this empty? See #108

}
]
},
"usability_domain": [
"This pipeline is well suited to analyze the small non-coding RNAs obtained from smallRNA-Seq, which enables the future researchers to understand the biological role of sncRNAs better. The pipeline integrates different modules and sources together, and is used to identify different types of sncRNAs, as well as predicting its biological roles and mRNA targets. ",
"Adapted from: Giurato, Giorgio, Maria Rosaria De Filippo, Antonio Rinaldi, Adnan Hashim, Giovanni Nassa, Maria Ravo, Francesca Rizzo, Roberta Tarallo, and Alessandro Weisz. “IMir: An Integrated Pipeline for High-Throughput Analysis of Small Non-Coding RNA Data Obtained by SmallRNA-Seq.” BMC Bioinformatics 14 (December 13, 2013): 362. https://doi.org/10.1186/1471-2105-14-362.",
"For all the tools with no version numbers provided, the most up-to-date versions are used. "
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Great job specifying this. 👍

],
"extension_domain": {},
"description_domain": {
"keywords": [
"Next Generation Sequencing",
"SmallRNA-Seq",
"data analysis pipeline",
"small non-coding RNA",
"microRNA",
"Piwi-interacting RNA"
],
"pipeline_steps": [
{
"name": "Cutadapt",
"version": "2.5",
"step_number": 1,
"input_list": [
{
"access_time": "2013-12-13T00:00:00-0500",
"uri": "www.example.com/iMirFiles/RNAinput.fastq",
"sha1_checksum": "000528checksum",
"filename": "RNA_input.fastq"
}
],
"output_list": [
{
"access_time": "2013-12-13T00:05:00-0500",
"uri": "www.example.com/iMirFiles/RNAinput.fa",
"sha1_checksum": "000528checksum",
"filename": "RNA_input_trimmed.fa"
}
],
"prerequisite": [
{
"name": "Python2.7_or_higher",
"uri": {
"access_time": "",
"uri": "https://www.python.org/getit/",
"sha1_checksum": "000528checksum",
"filename": ""
}
}
],
"description": "This is used for the pre-process analysis of the FASTQ files. The step is to remove duplicated RNA sequences in the library, and for quality filter analysis. Python is the pre-requisite to run this procedure"
},
{
"name": "miRanalyzer",
"version": "1.0",
"step_number": 2,
"input_list": [
{
"access_time": "2013-12-13T00:05:00-0500",
"uri": "www.example.com/iMirFiles/miRNA.rc",
"sha1_checksum": "000528checksum",
"filename": "miRNA.rc"
}
],
"output_list": [
{
"access_time": "2013-12-13T00:05:00-0500",
"uri": "www.example.com/iMirFiles/Sample_name_sncRNA_results/",
"sha1_checksum": "000528checksum",
"filename": "Sample_name_sncRNA_results (folder)"
}
],
"prerequisite": [
{
"name": "Bowtie",
"uri": {
"access_time": "",
"uri": "https://sourceforge.net/projects/bowtie-bio/files/bowtie/0.12.8/",
"sha1_checksum": "000528checksum",
"filename": ""
}
},
{
"name": "Vienna RNA Secondary Structure Package 1.8.5 or higher",
"uri": {
"access_time": "",
"uri": "https://www.tbi.univie.ac.at/RNA/",
"sha1_checksum": "000528checksum",
"filename": ""
}
},
{
"name": "Weka 3.5.3 or higher",
"uri": {
"access_time": "",
"uri": "https://sourceforge.net/projects/weka/files/weka-3-5/3.5.3/",
"sha1_checksum": "000528checksum",
"filename": ""
}
}
],
"description": "This step uses miRAnalyzer to map out inputs against known miRNA sequences. The goal is to detect the known miRNAs. "
},
{
"name": "DESeq",
"version": "1.10.1",
"step_number": 3,
"input_list": [
{
"access_time": "2013-12-13T00:05:00-0500",
"uri": "http://www.example.com/Case_Sample_vs_Control_Sample.dat",
"sha1_checksum": "000528checksum",
"filename": "Case_Sample_vs_control_Sample.dat"
}
],
"output_list": [
{
"access_time": "2013-12-13T00:05:00-0500",
"uri": "http://www.example.com/DESeq_comparison_results.txt",
"sha1_checksum": "000528checksum",
"filename": "DeSeq_comparison_results.txt"
}
],
"prerequisite": [
{
"name": "R 3.0.1 or higher",
"uri": {
"access_time": "",
"uri": "http://mirror.fcaglp.unlp.edu.ar/CRAN/",
"sha1_checksum": "000528checksum",
"filename": ""
}
}
],
"description": "This step is for differential expression analysis"
},
{
"name": "gplots",
"version": "3.0.1.1",
"step_number": 3,
"input_list": [],
"output_list": [],
"prerequisite": [],
"description": "gplots is used to generate plot for differential analysis and cluster analysis"
},
{
"name": "limma",
"version": "3.14.4",
"step_number": 3,
"input_list": [],
"output_list": [],
"prerequisite": [],
"description": "Limma is used to perform quantile normalization for differential expression analysis. "
},
{
"name": "No dependencies",
"version": "",
"step_number": 4,
"input_list": [],
"output_list": [],
"prerequisite": [],
"description": "The final step has no dependencies. TargetScan and miRanda are used, which are two different websites. TargetScan: http://www.targetscan.org/vert_72/. miRanda: http://www.microrna.org/microrna/home.do"
}
]
},
"execution_domain": {
"external_data_endpoints": [
{
"name": "MiRanda",
"url": "http://www.microrna.org/microrna/home.do"
},
{
"name": "miRanalyzer subsection 3.1",
"url": "https://bioinfo2.ugr.es/miRanalyzer/standalone.html#toc-Subsection-3.1"
}
],
"environment_variables": {},
"script_driver": "",
"software_prerequisites": [
{
"name": "Python",
"version": "2.7 or higher",
"uri": {
"access_time": "",
"uri": "https://www.python.org/getit/",
"sha1_checksum": "000528checksum",
"filename": ""
}
},
{
"name": "PERL",
"version": "5.0 or higher",
"uri": {
"access_time": "",
"uri": "http://www.perl.org/get.html",
"sha1_checksum": "000528checksum",
"filename": ""
}
},
{
"name": "Java",
"version": "1.6 or higher",
"uri": {
"access_time": "",
"uri": "http://www.java.com/en/download/",
"sha1_checksum": "000528checksum",
"filename": ""
}
},
{
"name": "R",
"version": "3.0.1 or higher",
"uri": {
"access_time": "",
"uri": "http://mirror.fcaglp.unlp.edu.ar/CRAN/",
"sha1_checksum": "000528checksum",
"filename": ""
}
},
{
"name": "gcc",
"version": "9.2",
"uri": {
"access_time": "",
"uri": "https://gcc.gnu.org/",
"sha1_checksum": "000528checksum",
"filename": ""
}
},
{
"name": "make",
"version": "4.2",
"uri": {
"access_time": "",
"uri": "http://ftp.gnu.org/gnu/make/",
"sha1_checksum": "000528checksum",
"filename": ""
}
},
{
"name": "g++",
"version": "2.69",
"uri": {
"access_time": "",
"uri": "https://launchpad.net/~ubuntu-toolchain-r/+archive/ubuntu/test",
"sha1_checksum": "000528checksum",
"filename": ""
}
}
],
"script": []
},
"parametric_domain": [
{
"step": "",
"param": "",
"value": ""
}
],
"io_domain": {
"input_subdomain": [
{
"uri": {
"access_time": "2013-12-13T00:00:00-0500",
"uri": "www.example.com/iMirFiles/iMirInputFiles.FASTQ",
"sha1_checksum": "000528checksum",
"filename": "iMirInputFiles.fastq"
}
}
],
"output_subdomain": [
{
"mediatype": "text/csv",
"uri": {
"access_time": "2013-12-13T00:00:00-0500",
"uri": "www.example.com/iMirFiles/SampleRNA_converted.rc",
"sha1_checksum": "000528checksum",
"filename": "SampleRNA_converted.rc"
}
},
{
"mediatype": "text/csv",
"uri": {
"access_time": "2013-12-13T00:00:00-0500",
"uri": "www.example.com/iMirFiles/trimmed_RNA.fa",
"sha1_checksum": "000528checksum",
"filename": "trimmed_RNA.fa"
}
},
{
"mediatype": "png",
"uri": {
"access_time": "2013-12-13T00:00:00-0500",
"uri": "www.example.com/iMirFiles/RNA_LengthDistribution.png",
"sha1_checksum": "000528checksum",
"filename": "RNA_LengthDistribution.png"
}
},
{
"mediatype": "text/csv",
"uri": {
"access_time": "2013-12-13T00:00:00-0500",
"uri": "www.example.com/iMirFiles/RNA_LengthDistribution.txt",
"sha1_checksum": "000528checksum",
"filename": "RNA_LengthDistribution.txt"
}
},
{
"mediatype": "folder",
"uri": {
"access_time": "2013-12-13T00:00:00-0500",
"uri": "www.example.com/iMirFiles/Finished_sncRNA_results/",
"sha1_checksum": "000528checksum",
"filename": "Finished_sncRNA_results (folder)"
}
}
]
},
"error_domain": {}
}