{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T04:14:29Z","timestamp":1684124069028},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Source Code Biol Med"],"published-print":{"date-parts":[[2007,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>This paper presents the Bioinformatics Computational Journal (BCJ), a framework for conducting and managing computational experiments in bioinformatics and computational biology. These experiments often involve series of computations, data searches, filters, and annotations which can benefit from a structured environment. Systems to manage computational experiments exist, ranging from libraries with standard data models to elaborate schemes to chain together input and output between applications. Yet, although such frameworks are available, their use is not widespread\u2013<jats:italic>ad hoc<\/jats:italic>scripts are often required to bind applications together. The BCJ explores another solution to this problem through a computer based environment suitable for on-site use, which builds on the traditional laboratory notebook paradigm. It provides an intuitive, extensible paradigm designed for expressive composition of applications. Extensive features facilitate sharing data, computational methods, and entire experiments. By focusing on the bioinformatics and computational biology domain, the scope of the computational framework was narrowed, permitting us to implement a capable set of features for this domain. This report discusses the features determined critical by our system and other projects, along with design issues. We illustrate the use of our implementation of the BCJ on two domain-specific examples.<\/jats:p>","DOI":"10.1186\/1751-0473-2-9","type":"journal-article","created":{"date-parts":[[2007,12,4]],"date-time":"2007-12-04T07:14:08Z","timestamp":1196752448000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Bioinformatics process management: information flow via a computational journal"],"prefix":"10.1186","volume":"2","author":[{"given":"Lance","family":"Feagan","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Justin","family":"Rohrer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander","family":"Garrett","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heather","family":"Amthauer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ed","family":"Komp","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam","family":"Hock","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Terry","family":"Clark","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerald","family":"Lushington","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gary","family":"Minden","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Victor","family":"Frost","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,12,3]]},"reference":[{"issue":"suppl_1","key":"17_CR1","doi-asserted-by":"publisher","first-page":"D21","DOI":"10.1093\/nar\/gkl986","volume":"35","author":"DA Benson","year":"2007","unstructured":"Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. Nucleic Acids Research. 2007, 35 (suppl_1): D21-25. 10.1093\/nar\/gkl986.","journal-title":"Nucleic Acids Research"},{"issue":"3","key":"17_CR2","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","volume":"215","author":"SF Altschul","year":"1990","unstructured":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. Journal of Molecular Biology. 1990, 215 (3): 403-410.","journal-title":"Journal of Molecular Biology"},{"issue":"6","key":"17_CR3","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000, 16 (6): 276-277. 10.1016\/S0168-9525(00)02024-2.","journal-title":"Trends Genet"},{"issue":"3","key":"17_CR4","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1093\/bib\/3.3.296","volume":"3","author":"H Mangalam","year":"2003","unstructured":"Mangalam H: The Bio* toolkits--a brief overview. Briefings in Bioinformatics. 2003, 3 (3): 296-302. 10.1093\/bib\/3.3.296.","journal-title":"Briefings in Bioinformatics"},{"issue":"3","key":"17_CR5","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1145\/1084805.1084807","volume":"34","author":"B Ludascher and Groble","year":"2005","unstructured":"Ludascher B: Introduction to the Special Section on Scientific Workflows. Sigmod Record. 2005, 34 (3): 3-4. 10.1145\/1084805.1084807.","journal-title":"Sigmod Record"},{"key":"17_CR6","first-page":"241","volume":"4","author":"Y Xu","year":"1996","unstructured":"Xu Y, Uberbacher EC: Gene prediction by pattern recognition and homology search. Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology; ISMB. 1996, 4: 241-251.","journal-title":"Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology; ISMB"},{"key":"17_CR7","volume-title":"The Java Developer's Guide to ELIPSE","author":"J D'Anjou","year":"2005","unstructured":"D'Anjou J, Fairbrother S, Kehn D, Kellerman J, McCarthy P: The Java Developer's Guide to ELIPSE. 2005, Boston , Addison-Wesley, 2nd","edition":"2nd"},{"key":"17_CR8","doi-asserted-by":"crossref","unstructured":"Simmhan YL, Plale B, Gannon D: A survey of data provenance in e-science. SIGMOD Record. 2005, ACM, 34 (3): 31-36. 10.1145\/1084805.1084812.","DOI":"10.1145\/1084805.1084812"},{"issue":"2","key":"17_CR9","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1147\/sj.402.0512","volume":"40","author":"SB Davidson","year":"2001","unstructured":"Davidson SB, Crabtree J, Brunk BP, Schug J, Tannen V, Overton GC, Stoeckert CJ: K2\/Kleisli and GUS: experiments in integrated access to genomic data sources. IBM Systems Journal. 2001, 40 (2): 512-531.","journal-title":"IBM Systems Journal"},{"key":"17_CR10","unstructured":"Document Type Definition for XML data. [http:\/\/silk.bioinfo.ittc.ku.edu\/cj\/schema\/ResourceDef.dtd]"},{"issue":"1","key":"17_CR11","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1093\/bioinformatics\/17.1.73","volume":"17","author":"C Letondal","year":"2001","unstructured":"Letondal C: A Web interface generator for molecular biology programs in Unix. Bioinformatics. 2001, 17 (1): 73-82. 10.1093\/bioinformatics\/17.1.73.","journal-title":"Bioinformatics"},{"key":"17_CR12","volume-title":"Bioinformatics Computational Journal: User Guide, Technical Report ITTC-FY2008-TR-38270-04","author":"V Frost","year":"2007","unstructured":"Frost V, Clark T, Gauch S, Lushington G, Minden G, Komp E, Hock A, Johnson D, Feagan L, Garrett A, Rohrer J, Amthauer H, Ozor A: Bioinformatics Computational Journal: User Guide, Technical Report ITTC-FY2008-TR-38270-04. 2007, [http:\/\/www.ittc.ku.edu\/publications\/documents\/Bioinfo_Comp_Journal_User_Manual.pdf]"},{"key":"17_CR13","unstructured":"GROMACS: Fast, Free and Flexible MD. [http:\/\/www.gromacs.org]"},{"key":"17_CR14","unstructured":"Molecular Dynamics Tutorial (GROMACS). [http:\/\/md.chem.rug.nl\/education\/mdcourse\/index.html]"},{"issue":"1","key":"17_CR15","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W Humphrey","year":"1996","unstructured":"Humphrey W, Dalke A, Schulten K: VMD: visual molecular dynamics. Journal of Molecular Graphics. 1996, 14 (1): 33-38. 10.1016\/0263-7855(96)00018-5.","journal-title":"Journal of Molecular Graphics"},{"issue":"1","key":"17_CR16","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1089\/153623103322006661","volume":"7","author":"JD Eckart","year":"2003","unstructured":"Eckart JD, Sobral B: A Life Scientists Gateway to Distributed Data Management and Computing: The PathPort\/ToolBus Framework. OMICS: A Journal of Integrative Biology. 2003, 7 (1): 79-88. 10.1089\/153623103322006661.","journal-title":"OMICS: A Journal of Integrative Biology"},{"key":"17_CR17","first-page":"242","volume-title":"BioCoRE: a collaboratory for structural biology: San Francisco, California.","author":"M Bhandarkar","year":"1999","unstructured":"Bhandarkar M, Budescu G, Humphrey WF, Izaguirre JA, Izrailev S, Kal LV, Kosztin D, Molnar F, Phillips JC, Schulten K: BioCoRE: a collaboratory for structural biology: San Francisco, California.1999, , 242-251."},{"issue":"16","key":"17_CR18","doi-asserted-by":"publisher","first-page":"1781","DOI":"10.1002\/jcc.20289","volume":"26","author":"JC Phillips","year":"2005","unstructured":"Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K: Scalable molecular dynamics with NAMD. J Comput Chem. 2005, 26 (16): 1781-1802. 10.1002\/jcc.20289.","journal-title":"J Comput Chem"},{"key":"17_CR19","unstructured":"VMD - Visual Molecular Dynamics. [http:\/\/www.ks.uiuc.edu\/Research\/vmd\/]"},{"issue":"1","key":"17_CR20","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1093\/bioinformatics\/17.1.73","volume":"17","author":"C Letondal","year":"2001","unstructured":"Letondal C: A web interface generator for molecular biology programs in Unix. Bioinformatics (Oxford, England). 2001, 17 (1): 73-82. 10.1093\/bioinformatics\/17.1.73.","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"34W1","key":"17_CR21","first-page":"5","volume":"1","author":"M Rampp Soddemann","year":"2006","unstructured":"Rampp M: The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. Nucleic Acids Research. 2006, 1 (34W1): 5-9.","journal-title":"Nucleic Acids Research"},{"key":"17_CR22","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1186\/1471-2105-5-40","volume":"5","author":"SP Shah","year":"2004","unstructured":"Shah SP, He DY, Sawkins JN, Druce JC, Quon G, Lett D, Zheng GX, Xu T, Ouellette BF: Pegasys: software for executing and integrating analyses of biological sequences. BMC Bioinformatics. 2004, 5: 40-10.1186\/1471-2105-5-40.","journal-title":"BMC Bioinformatics"},{"issue":"Suppl 1","key":"17_CR23","doi-asserted-by":"publisher","first-page":"i302","DOI":"10.1093\/bioinformatics\/btg1041","volume":"19","author":"RD Stevens","year":"2003","unstructured":"Stevens RD, Robinson AJ, Goble CA: myGrid: personalised bioinformatics on the information grid. Bioinformatics (Oxford, England). 2003, 19 Suppl 1: i302-4. 10.1093\/bioinformatics\/btg1041.","journal-title":"Bioinformatics (Oxford, England)"},{"key":"17_CR24","unstructured":"SciTegic: SciTegic - PP Overview. [http:\/\/www.scitegic.com\/products\/overview\/]"},{"key":"17_CR25","first-page":"Poster","volume-title":"Genome Informatics 2005 (Cold Spring Harbor Laboratory, New York)","author":"SV Angiuol","year":"2006","unstructured":"Angiuol SV: Workflow \/ Ergatis: A Data Management System for Automated Genome Annotation and Comparative Analysis (poster). Genome Informatics 2005 (Cold Spring Harbor Laboratory, New York). 2006, Poster."},{"issue":"8","key":"17_CR26","doi-asserted-by":"crossref","first-page":"1904","DOI":"10.1101\/gr.1363103","volume":"13","author":"S Hoon","year":"2003","unstructured":"Hoon S, Ratnapu KK, Chia JM, Kumarasamy B, Juguang X, Clamp M, Stabenau A, Potter S, Clarke L, Stupka E: Biopipe: a flexible framework for protocol-based bioinformatics analysis. Genome Res. 2003, 13 (8): 1904-1915.","journal-title":"Genome Res"},{"key":"17_CR27","unstructured":"SCIRun - SCI Software - Scientific Computing and Imaging Institute. [http:\/\/software.sci.utah.edu\/scirun.html]"},{"key":"17_CR28","unstructured":"Data mining, Clementine, Predictive Modeling, Predictive Analytics, Predictive Analysis. [http:\/\/www.spss.com\/clementine]"}],"container-title":["Source Code for Biology and Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1751-0473-2-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T03:33:17Z","timestamp":1684121597000},"score":1,"resource":{"primary":{"URL":"https:\/\/scfbm.biomedcentral.com\/articles\/10.1186\/1751-0473-2-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,12]]},"references-count":28,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["17"],"URL":"https:\/\/doi.org\/10.1186\/1751-0473-2-9","relation":{},"ISSN":["1751-0473"],"issn-type":[{"value":"1751-0473","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,12]]},"assertion":[{"value":"21 January 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 December 2007","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 December 2007","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"9"}}