Source Code for Biology and Medicine最新文献

{"title":"FLIM-FRET analyzer: open source software for automation of lifetime-based FRET analysis.","authors":"Jiho Kim,&nbsp;Yury Tsoy,&nbsp;Jan Persson,&nbsp;Regis Grailhe","doi":"10.1186/s13029-017-0067-0","DOIUrl":"https://doi.org/10.1186/s13029-017-0067-0","url":null,"abstract":"<p><strong>Background: </strong>Despite the broad use of FRET techniques, available methods for analyzing protein-protein interaction are subject to high labor and lack of systematic analysis. We propose an open source software allowing the quantitative analysis of fluorescence lifetime imaging (FLIM) while integrating the steady-state fluorescence intensity information for protein-protein interaction studies.</p><p><strong>Findings: </strong>Our developed open source software is dedicated to fluorescence lifetime imaging microscopy (FLIM) data obtained from Becker & Hickl SPC-830. FLIM-FRET analyzer includes: a user-friendly interface enabling automated intensity-based segmentation into single cells, time-resolved fluorescence data fitting to lifetime value for each segmented objects, batch capability, and data representation with donor lifetime versus acceptor/donor intensity quantification as a measure of protein-protein interactions.</p><p><strong>Conclusions: </strong>The FLIM-FRET analyzer software is a flexible application for lifetime-based FRET analysis. The application, the C#. NET source code, and detailed documentation are freely available at the following URL: http://FLIM-analyzer.ip-korea.org.</p>","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":"12 ","pages":"7"},"PeriodicalIF":0.0,"publicationDate":"2017-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13029-017-0067-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35253713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"goSTAG: gene ontology subtrees to tag and annotate genes within a set.","authors":"Brian D Bennett,&nbsp;Pierre R Bushel","doi":"10.1186/s13029-017-0066-1","DOIUrl":"https://doi.org/10.1186/s13029-017-0066-1","url":null,"abstract":"<p><strong>Background: </strong>Over-representation analysis (ORA) detects enrichment of genes within biological categories. Gene Ontology (GO) domains are commonly used for gene/gene-product annotation. When ORA is employed, often times there are hundreds of statistically significant GO terms per gene set. Comparing enriched categories between a large number of analyses and identifying the term within the GO hierarchy with the most connections is challenging. Furthermore, ascertaining biological themes representative of the samples can be highly subjective from the interpretation of the enriched categories.</p><p><strong>Results: </strong>We developed goSTAG for utilizing GO Subtrees to Tag and Annotate Genes that are part of a set. Given gene lists from microarray, RNA sequencing (RNA-Seq) or other genomic high-throughput technologies, goSTAG performs GO enrichment analysis and clusters the GO terms based on the <i>p</i>-values from the significance tests. GO subtrees are constructed for each cluster, and the term that has the most paths to the root within the subtree is used to tag and annotate the cluster as the biological theme. We tested goSTAG on a microarray gene expression data set of samples acquired from the bone marrow of rats exposed to cancer therapeutic drugs to determine whether the combination or the order of administration influenced bone marrow toxicity at the level of gene expression. Several clusters were labeled with GO biological processes (BPs) from the subtrees that are indicative of some of the prominent pathways modulated in bone marrow from animals treated with an oxaliplatin/topotecan combination. In particular, negative regulation of MAP kinase activity was the biological theme exclusively in the cluster associated with enrichment at 6 h after treatment with oxaliplatin followed by control. However, nucleoside triphosphate catabolic process was the GO BP labeled exclusively at 6 h after treatment with topotecan followed by control.</p><p><strong>Conclusions: </strong>goSTAG converts gene lists from genomic analyses into biological themes by enriching biological categories and constructing GO subtrees from over-represented terms in the clusters. The terms with the most paths to the root in the subtree are used to represent the biological themes. goSTAG is developed in R as a Bioconductor package and is available at https://bioconductor.org/packages/goSTAG.</p>","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":"12 ","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2017-04-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13029-017-0066-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34916266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"LitDB - Keeping Track of Research Papers From Your Institute Made Simple.","authors":"Jörn Bethune,&nbsp;Lars Kraemer,&nbsp;Ingo Thomsen,&nbsp;Andreas Keller,&nbsp;David Ellinghaus,&nbsp;Andre Franke","doi":"10.1186/s13029-017-0065-2","DOIUrl":"https://doi.org/10.1186/s13029-017-0065-2","url":null,"abstract":"<p><strong>Background: </strong>In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their scientific publications. However, in most institutions and universities articles are often managed in a redundant file-based and non-central way. Whereas excellent reference management software packages such as Zotero, Endnote or Mendeley exist to manage bibliographies and references when writing scientific articles, we are not aware of any open source database solution keeping track of publication records from large scientific groups, entire institutions and/or universities.</p><p><strong>Results: </strong>We here describe LitDB, a novel open source literature database solution for easy maintenance of publication lists assigned to various topics. In the last 2 years more than 50 users have been using LitDB at our research institute. The LitDB system is accessed via a web browser. Publications can be uploaded through direct exports from reference manager libraries or by entering PubMed IDs. Single users or user groups can track their citation counts, h-index and impact factor statistics and gain insights into the publication records of other users. It offers various visualization functions like coauthor networks and provides ways to organize publications from dedicated projects and user groups. The latter is in particular beneficial to manage publication lists of large research groups and research initiatives through a \"crowd-sourcing\" effort.</p><p><strong>Conclusions: </strong>Keeping track of papers authored and published by a research group, institute or university is an important and non-trivial task. By using a centralized web-based platform for publication management such as LitDB the compilation of project- and group-related publication lists becomes easily manageable and it is less likely that papers are forgotten along the way.</p>","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":"12 ","pages":"5"},"PeriodicalIF":0.0,"publicationDate":"2017-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13029-017-0065-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34857366","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NET: a new framework for the vectorization and examination of network data","authors":"J. Lasser, E. Katifori","doi":"10.1186/s13029-017-0064-3","DOIUrl":"https://doi.org/10.1186/s13029-017-0064-3","url":null,"abstract":"","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13029-017-0064-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43129691","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Algorithm and software to automatically identify latency and amplitude features of local field potentials recorded in electrophysiological investigation","authors":"M. Rubega, C. Cecchetto, S. Vassanelli, G. Sparacino","doi":"10.1186/s13029-017-0062-5","DOIUrl":"https://doi.org/10.1186/s13029-017-0062-5","url":null,"abstract":"","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13029-017-0062-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47567721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DEApp: an interactive web interface for differential expression analysis of next generation sequence data","authors":"Yan Li, J. Andrade","doi":"10.1186/s13029-017-0063-4","DOIUrl":"https://doi.org/10.1186/s13029-017-0063-4","url":null,"abstract":"","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":"33 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13029-017-0063-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41295371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum to: A bedr way of genomic interval processing","authors":"Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu, P. Boutros","doi":"10.1186/s13029-016-0061-y","DOIUrl":"https://doi.org/10.1186/s13029-016-0061-y","url":null,"abstract":"","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13029-016-0061-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46605085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A bedr way of genomic interval processing","authors":"Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei-Fei Liu, P. Boutros","doi":"10.1186/s13029-016-0059-5","DOIUrl":"https://doi.org/10.1186/s13029-016-0059-5","url":null,"abstract":"","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13029-016-0059-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65752540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PureCN: copy number calling and SNV classification using targeted short read sequencing","authors":"Markus Riester, Angad P. Singh, A. R. Brannon, Kun Yu, C. D. Campbell, Derek Y. Chiang, Michael P. Morrissey","doi":"10.1186/s13029-016-0060-z","DOIUrl":"https://doi.org/10.1186/s13029-016-0060-z","url":null,"abstract":"","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13029-016-0060-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65752963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.","authors":"Toshiki Takeuchi,&nbsp;Atsuo Yamada,&nbsp;Takashi Aoki,&nbsp;Kunihiro Nishimura","doi":"10.1186/s13029-016-0058-6","DOIUrl":"https://doi.org/10.1186/s13029-016-0058-6","url":null,"abstract":"<p><strong>Background: </strong>Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast. However, SAMtools requires an additional implementation to be used in parallel with, for example, OpenMP (Open Multi-Processing) libraries. For the accumulation of next-generation sequencing data, a simple parallelization program, which can support cloud and PC cluster environments, is required.</p><p><strong>Results: </strong>We have developed cljam using the Clojure programming language, which simplifies parallel programming, to handle SAM/BAM data. Cljam can run in a Java runtime environment (e.g., Windows, Linux, Mac OS X) with Clojure.</p><p><strong>Conclusions: </strong>Cljam can process and analyze SAM/BAM files in parallel and at high speed. The execution time with cljam is almost the same as with SAMtools. The cljam code is written in Clojure and has fewer lines than other similar tools.</p>","PeriodicalId":35052,"journal":{"name":"Source Code for Biology and Medicine","volume":" ","pages":"12"},"PeriodicalIF":0.0,"publicationDate":"2016-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13029-016-0058-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34316962","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}