{"title":"Log::ProgramInfo：用于收集和记录生物信息学管道数据的 Perl 模块。","authors":"John M Macdonald, Paul C Boutros","doi":"10.1186/s13029-016-0055-9","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>To reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results.</p><p><strong>Results: </strong>Log::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution. It can also be used to compare the environments of two executions to determine whether there were any differences that might affect (or explain) their operation.</p><p><strong>Availability: </strong>The source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/).</p><p><strong>Conclusion: </strong>Using Log::ProgramInfo in programs creating result data for publishable research, and including the Log::ProgramInfo output log as part of the publication of that research is a valuable method to assist others to duplicate the programming environment as a precursor to validating and/or extending that research.</p>","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":" ","pages":"9"},"PeriodicalIF":0.0000,"publicationDate":"2016-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919834/pdf/","citationCount":"0","resultStr":"{\"title\":\"Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines.\",\"authors\":\"John M Macdonald, Paul C Boutros\",\"doi\":\"10.1186/s13029-016-0055-9\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>To reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results.</p><p><strong>Results: </strong>Log::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution. It can also be used to compare the environments of two executions to determine whether there were any differences that might affect (or explain) their operation.</p><p><strong>Availability: </strong>The source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/).</p><p><strong>Conclusion: </strong>Using Log::ProgramInfo in programs creating result data for publishable research, and including the Log::ProgramInfo output log as part of the publication of that research is a valuable method to assist others to duplicate the programming environment as a precursor to validating and/or extending that research.</p>\",\"PeriodicalId\":35052,\"journal\":{\"name\":\"Source Code for Biology and Medicine\",\"volume\":\" \",\"pages\":\"9\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2016-06-24\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4919834/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Source Code for Biology and Medicine\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1186/s13029-016-0055-9\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2016/1/1 0:00:00\",\"PubModel\":\"eCollection\",\"JCR\":\"Q2\",\"JCRName\":\"Decision Sciences\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Source Code for Biology and Medicine","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1186/s13029-016-0055-9","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2016/1/1 0:00:00","PubModel":"eCollection","JCR":"Q2","JCRName":"Decision Sciences","Score":null,"Total":0}
Log::ProgramInfo: A Perl module to collect and log data for bioinformatics pipelines.
Background: To reproduce and report a bioinformatics analysis, it is important to be able to determine the environment in which a program was run. It can also be valuable when trying to debug why different executions are giving unexpectedly different results.
Results: Log::ProgramInfo is a Perl module that writes a log file at the termination of execution of the enclosing program, to document useful execution characteristics. This log file can be used to re-create the environment in order to reproduce an earlier execution. It can also be used to compare the environments of two executions to determine whether there were any differences that might affect (or explain) their operation.
Availability: The source is available on CPAN (Macdonald and Boutros, Log-ProgramInfo. http://search.cpan.org/~boutroslb/Log-ProgramInfo/).
Conclusion: Using Log::ProgramInfo in programs creating result data for publishable research, and including the Log::ProgramInfo output log as part of the publication of that research is a valuable method to assist others to duplicate the programming environment as a precursor to validating and/or extending that research.
期刊介绍：
Source Code for Biology and Medicine is a peer-reviewed open access, online journal that publishes articles on source code employed over a wide range of applications in biology and medicine. The journal"s aim is to publish source code for distribution and use in the public domain in order to advance biological and medical research. Through this dissemination, it may be possible to shorten the time required for solving certain computational problems for which there is limited source code availability or resources.
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