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Juntian Wei BCO submission.md #176
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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", | ||
"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" | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Incorrect contribution type. Please modify. See #148 |
||
], | ||
"name": "Janisha Patel", | ||
"email": "janishapatel@gwu.edu" | ||
}, | ||
"date": "10_16_2019" | ||
} | ||
], | ||
"contributors": [ | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Why are the publication authors not added as contributors? See #113 |
||
{ | ||
"name": "", | ||
"orcid": "", | ||
"affiliation": "", | ||
"contribution": [ | ||
"createdBy" | ||
], | ||
"email": "jwei48@gwmail.gwu.edu" | ||
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There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Why is this empty? See #108 |
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} | ||
] | ||
}, | ||
"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. " | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Great job specifying this. 👍 |
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], | ||
"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": {} | ||
} |
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good job fixing version.