TY - JOUR AU - Weber, G. M. AU - Mandl, K. D. AU - Kohane, I. S. PY - 2014 DA - 2014// TI - Finding the missing link for big biomedical data JO - JAMA VL - 311 ID - Weber2014 ER - TY - STD TI - Hemingway H, Asselbergs FW, Danesh J, Dobson R, Maniadakis N, Maggioni A, Ghislaine JM, van Thiel MC, Brobert G, Vardas P, Anker SD, Grobbee DE, Denaxas S. On behalf of the Innovative Medicines Initiative 2nd programme, Big Data for Better Outcomes, BigData@Heart Consortium. Big data from electronic health records for early and late translational cardiovascular research: challenges and potential. Eur Heart J. 2017:ehx487. https://doi.org/10.1093/eurheartj/ehx487. UR - https://doi.org/10.1093/eurheartj/ehx487 ID - ref2 ER - TY - JOUR AU - Denaxas, S. C. AU - George, J. AU - Herrett, E. AU - Shah, A. D. AU - Kalra, D. AU - Hingorani, A. D. AU - Kivimaki, M. AU - Timmis, A. D. AU - Smeeth, L. AU - Hemingway, H. PY - 2012 DA - 2012// TI - Data resource profile: cardiovascular disease research using linked bespoke studies and electronic health records (caliber) JO - Int J Epidemiol VL - 41 UR - https://doi.org/10.1093/ije/dys188 DO - 10.1093/ije/dys188 ID - Denaxas2012 ER - TY - JOUR AU - Collins, F. S. AU - Varmus, H. PY - 2015 DA - 2015// TI - A new initiative on precision medicine JO - N Engl J Med VL - 372 UR - https://doi.org/10.1056/NEJMp1500523 DO - 10.1056/NEJMp1500523 ID - Collins2015 ER - TY - JOUR AU - Sudlow, C. AU - Gallacher, J. AU - Allen, N. AU - Beral, V. AU - Burton, P. AU - Danesh, J. AU - Downey, P. AU - Elliott, P. AU - Green, J. AU - Landray, M. PY - 2015 DA - 2015// TI - Uk biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age JO - PLoS Med VL - 12 UR - https://doi.org/10.1371/journal.pmed.1001779 DO - 10.1371/journal.pmed.1001779 ID - Sudlow2015 ER - TY - JOUR AU - Gottesman, O. AU - Kuivaniemi, H. AU - Tromp, G. AU - Faucett, W. A. AU - Li, R. AU - Manolio, T. A. AU - Sanderson, S. C. AU - Kannry, J. AU - Zinberg, R. AU - Basford, M. A. PY - 2013 DA - 2013// TI - The electronic medical records and genomics (emerge) network: past, present, and future JO - Genet Med VL - 15 UR - https://doi.org/10.1038/gim.2013.72 DO - 10.1038/gim.2013.72 ID - Gottesman2013 ER - TY - JOUR AU - Crosslin, D. R. AU - McDavid, A. AU - Weston, N. AU - Nelson, S. C. AU - Zheng, X. AU - Hart, E. AU - De Andrade, M. AU - Kullo, I. J. AU - McCarty, C. A. AU - Doheny, K. F. PY - 2012 DA - 2012// TI - Genetic variants associated with the white blood cell count in 13,923 subjects in the emerge network JO - Hum Genet VL - 131 UR - https://doi.org/10.1007/s00439-011-1103-9 DO - 10.1007/s00439-011-1103-9 ID - Crosslin2012 ER - TY - JOUR AU - Timmis, A. AU - Rapsomaniki, E. AU - Chung, S. AU - Pujades-Rodriguez, M. AU - Moayyeri, A. AU - Stogiannis, D. AU - Shah, A. AU - Pasea, L. AU - Denaxas, S. AU - Emmas, C. PY - 2016 DA - 2016// TI - Prolonged dual antiplatelet therapy in stable coronary disease: comparative observational study of benefits and harms in unselected versus trial populations JO - Bmj VL - 353 UR - https://doi.org/10.1136/bmj.i3163 DO - 10.1136/bmj.i3163 ID - Timmis2016 ER - TY - JOUR AU - Shah, A. D. AU - Langenberg, C. AU - Rapsomaniki, E. AU - Denaxas, S. AU - Pujades-Rodriguez, M. AU - Gale, C. P. AU - Deanfield, J. AU - Smeeth, L. AU - Timmis, A. AU - Hemingway, H. PY - 2015 DA - 2015// TI - Type 2 diabetes and incidence of cardiovascular diseases: a cohort study in 1· 9 million people JO - Lancet Diabetes Endocrinol VL - 3 UR - https://doi.org/10.1016/S2213-8587(14)70219-0 DO - 10.1016/S2213-8587(14)70219-0 ID - Shah2015 ER - TY - JOUR AU - Rapsomaniki, E. AU - Timmis, A. AU - George, J. AU - Pujades-Rodriguez, M. AU - Shah, A. D. AU - Denaxas, S. AU - White, I. R. AU - Caulfield, M. J. AU - Deanfield, J. E. AU - Smeeth, L. PY - 2014 DA - 2014// TI - Blood pressure and incidence of twelve cardiovascular diseases: lifetime risks, healthy life-years lost, and age-specific associations in 1· 25 million people JO - Lancet VL - 383 UR - https://doi.org/10.1016/S0140-6736(14)60685-1 DO - 10.1016/S0140-6736(14)60685-1 ID - Rapsomaniki2014 ER - TY - JOUR AU - Rapsomaniki, E. AU - Shah, A. AU - Perel, P. AU - Denaxas, S. AU - George, J. AU - Nicholas, O. AU - Udumyan, R. AU - Feder, G. S. AU - Hingorani, A. D. AU - Timmis, A. PY - 2013 DA - 2013// TI - Prognostic models for stable coronary artery disease based on electronic health record cohort of 102 023 patients JO - Eur Heart J VL - 35 UR - https://doi.org/10.1093/eurheartj/eht533 DO - 10.1093/eurheartj/eht533 ID - Rapsomaniki2013 ER - TY - JOUR AU - Kho, A. N. AU - Pacheco, J. A. AU - Peissig, P. L. AU - Rasmussen, L. AU - Newton, K. M. AU - Weston, N. AU - Crane, P. K. AU - Pathak, J. AU - Chute, C. G. AU - Bielinski, S. J. PY - 2011 DA - 2011// TI - Electronic medical records for genetic research: results of the emerge consortium JO - Sci Transl Med VL - 3 UR - https://doi.org/10.1126/scitranslmed.3001807 DO - 10.1126/scitranslmed.3001807 ID - Kho2011 ER - TY - STD TI - Koudstaal S, Pujades-Rodriguez M, Denaxas S, Gho JMIH, Shah AD, Yu N, Patel RS, Gale CP, Hoes AW, Cleland JG, Asselbergs FW, Hemingway H. Prognostic burden of heart failure recorded in primary care, acute hospital admissions, or both: a population-based linked electronic health record cohort study in 2.1 million people. Eur J Heart Fail. 2016. doi:10.1002/ejhf.709. UR - http://dx.doi.org/10.1002/ejhf.709 ID - ref13 ER - TY - JOUR AU - Bell, S. AU - Daskalopoulou, M. AU - Rapsomaniki, E. AU - George, J. AU - Britton, A. AU - Bobak, M. AU - Casas, J. P. AU - Dale, C. E. AU - Denaxas, S. AU - Shah, A. D. PY - 2017 DA - 2017// TI - Association between clinically recorded alcohol consumption and initial presentation of 12 cardiovascular diseases: population based cohort study using linked health records JO - Bmj VL - 356 UR - https://doi.org/10.1136/bmj.j909 DO - 10.1136/bmj.j909 ID - Bell2017 ER - TY - JOUR AU - McNutt, M. PY - 2014 DA - 2014// TI - Reproducibility JO - Science VL - 343 UR - https://doi.org/10.1126/science.1250475 DO - 10.1126/science.1250475 ID - McNutt2014 ER - TY - JOUR AU - Begley, C. G. AU - Ioannidis, J. P. PY - 2015 DA - 2015// TI - Reproducibility in science JO - Circ Res VL - 116 UR - https://doi.org/10.1161/CIRCRESAHA.114.303819 DO - 10.1161/CIRCRESAHA.114.303819 ID - Begley2015 ER - TY - JOUR AU - Iqbal, S. A. AU - Wallach, J. D. AU - Khoury, M. J. AU - Schully, S. D. AU - Ioannidis, J. P. PY - 2016 DA - 2016// TI - Reproducible research practices and transparency across the biomedical literature JO - PLoS Biol VL - 14 UR - https://doi.org/10.1371/journal.pbio.1002333 DO - 10.1371/journal.pbio.1002333 ID - Iqbal2016 ER - TY - JOUR AU - Springate, D. A. AU - Kontopantelis, E. AU - Ashcroft, D. M. AU - Olier, I. AU - Parisi, R. AU - Chamapiwa, E. AU - Reeves, D. PY - 2014 DA - 2014// TI - Clinicalcodes: an online clinical codes repository to improve the validity and reproducibility of research using electronic medical records JO - PloS ONE VL - 9 UR - https://doi.org/10.1371/journal.pone.0099825 DO - 10.1371/journal.pone.0099825 ID - Springate2014 ER - TY - JOUR AU - Vezyridis, P. AU - Timmons, S. PY - 2016 DA - 2016// TI - Evolution of primary care databases in uk: a scientometric analysis of research output JO - BMJ Open VL - 6 UR - https://doi.org/10.1136/bmjopen-2016-012785 DO - 10.1136/bmjopen-2016-012785 ID - Vezyridis2016 ER - TY - JOUR AU - Goodman, S. N. AU - Fanelli, D. AU - Ioannidis, J. P. PY - 2016 DA - 2016// TI - What does research reproducibility mean? JO - Sci Transl Med VL - 8 UR - https://doi.org/10.1126/scitranslmed.aaf5027 DO - 10.1126/scitranslmed.aaf5027 ID - Goodman2016 ER - TY - JOUR AU - Donnelly, K. PY - 2006 DA - 2006// TI - Snomed-ct: The advanced terminology and coding system for ehealth JO - Stud Health Technol Inform VL - 121 ID - Donnelly2006 ER - TY - JOUR AU - Denaxas, S. C. AU - Asselbergs, F. W. AU - Moore, J. H. PY - 2016 DA - 2016// TI - The tip of the iceberg: challenges of accessing hospital electronic health record data for biological data mining JO - BioData Min VL - 9 UR - https://doi.org/10.1186/s13040-016-0109-1 DO - 10.1186/s13040-016-0109-1 ID - Denaxas2016 ER - TY - JOUR AU - Denaxas, S. C. AU - Morley, K. I. PY - 2015 DA - 2015// TI - Big biomedical data and cardiovascular disease research: opportunities and challenges JO - Eur Heart J-Qual Care Clin Outcome VL - 1 UR - https://doi.org/10.1093/ehjqcco/qcv005 DO - 10.1093/ehjqcco/qcv005 ID - Denaxas2015 ER - TY - JOUR AU - Hripcsak, G. AU - Albers, D. J. PY - 2013 DA - 2013// TI - Next-generation phenotyping of electronic health records JO - J Am Med Inform Assoc VL - 20 UR - https://doi.org/10.1136/amiajnl-2012-001145 DO - 10.1136/amiajnl-2012-001145 ID - Hripcsak2013 ER - TY - JOUR AU - Newton, K. M. AU - Peissig, P. L. AU - Kho, A. N. AU - Bielinski, S. J. AU - Berg, R. L. AU - Choudhary, V. AU - Basford, M. AU - Chute, C. G. AU - Kullo, I. J. AU - Li, R. PY - 2013 DA - 2013// TI - Validation of electronic medical record-based phenotyping algorithms: results and lessons learned from the emerge network JO - J Am Med Inform Assoc VL - 20 UR - https://doi.org/10.1136/amiajnl-2012-000896 DO - 10.1136/amiajnl-2012-000896 ID - Newton2013 ER - TY - JOUR AU - Stein, L. PY - 2002 DA - 2002// TI - Creating a bioinformatics nation JO - Nature VL - 417 UR - https://doi.org/10.1038/417119a DO - 10.1038/417119a ID - Stein2002 ER - TY - JOUR AU - Benchimol, E. I. AU - Smeeth, L. AU - Guttmann, A. AU - Harron, K. AU - Moher, D. AU - Petersen, I. AU - Sørensen, H. T. AU - von Elm, E. AU - Langan, S. M. AU - Committee, R. W. PY - 2015 DA - 2015// TI - The reporting of studies conducted using observational routinely-collected health data (record) statement JO - PLoS Med VL - 12 UR - https://doi.org/10.1371/journal.pmed.1001885 DO - 10.1371/journal.pmed.1001885 ID - Benchimol2015 ER - TY - STD TI - REporting of Studies Conducted Using Observational Routinely-collected Data (RECORD). http://www.recordstatement.org/. Accessed 28 July 2017. UR - http://www.recordstatement.org/ ID - ref28 ER - TY - JOUR AU - Von Elm, E. AU - Altman, D. G. AU - Egger, M. AU - Pocock, S. J. AU - Gøtzsche, P. C. AU - Vandenbroucke, J. P. AU - Initiative, S. PY - 2014 DA - 2014// TI - The strengthening the reporting of observational studies in epidemiology (STROBE) statement: guidelines for reporting observational studies JO - Int J Surg VL - 12 UR - https://doi.org/10.1016/j.ijsu.2014.07.013 DO - 10.1016/j.ijsu.2014.07.013 ID - Von Elm2014 ER - TY - STD TI - STrengthening the Reporting of OBservational Studies in Epidemiology (STROBE). https://www.strobe-statement.org/. Accessed 28 July 2017. UR - https://www.strobe-statement.org/ ID - ref30 ER - TY - JOUR AU - Davison, A. PY - 2012 DA - 2012// TI - Automated capture of experiment context for easier reproducibility in computational research JO - Comput Sci Eng VL - 14 UR - https://doi.org/10.1109/MCSE.2012.41 DO - 10.1109/MCSE.2012.41 ID - Davison2012 ER - TY - JOUR AU - Sandve, G. K. AU - Nekrutenko, A. AU - Taylor, J. AU - Hovig, E. PY - 2013 DA - 2013// TI - Ten simple rules for reproducible computational research JO - PLoS Comput Biol VL - 9 UR - https://doi.org/10.1371/journal.pcbi.1003285 DO - 10.1371/journal.pcbi.1003285 ID - Sandve2013 ER - TY - JOUR AU - Mesirov, J. P. PY - 2010 DA - 2010// TI - Accessible reproducible research JO - Science VL - 327 UR - https://doi.org/10.1126/science.1179653 DO - 10.1126/science.1179653 ID - Mesirov2010 ER - TY - JOUR AU - Tan, T. W. AU - Tong, J. C. AU - Khan, A. M. AU - de Silva, M. AU - Lim, K. S. AU - Ranganathan, S. PY - 2010 DA - 2010// TI - Advancing standards for bioinformatics activities: persistence, reproducibility, disambiguation and minimum information about a bioinformatics investigation (miabi) JO - BMC Genom VL - 11 UR - https://doi.org/10.1186/1471-2164-11-S4-S27 DO - 10.1186/1471-2164-11-S4-S27 ID - Tan2010 ER - TY - JOUR AU - Ravel, J. AU - Wommack, K. E. PY - 2014 DA - 2014// TI - All hail reproducibility in microbiome research JO - Microbiome VL - 2 UR - https://doi.org/10.1186/2049-2618-2-8 DO - 10.1186/2049-2618-2-8 ID - Ravel2014 ER - TY - JOUR AU - Peng, R. PY - 2009 DA - 2009// TI - Reproducible research and biostatistics JO - Biostatistics VL - 10 UR - https://doi.org/10.1093/biostatistics/kxp014 DO - 10.1093/biostatistics/kxp014 ID - Peng2009 ER - TY - JOUR AU - Gorgolewski, K. J. AU - Alfaro-Almagro, F. AU - Auer, T. AU - Bellec, P. AU - Capotă, M. AU - Chakravarty, M. M. AU - Churchill, N. W. AU - Cohen, A. L. AU - Craddock, R. C. AU - Devenyi, G. A. PY - 2017 DA - 2017// TI - Bids apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods JO - PLoS Comput Biol VL - 13 UR - https://doi.org/10.1371/journal.pcbi.1005209 DO - 10.1371/journal.pcbi.1005209 ID - Gorgolewski2017 ER - TY - JOUR AU - Waltemath, D. AU - Adams, R. AU - Bergmann, F. T. AU - Hucka, M. AU - Kolpakov, F. AU - Miller, A. K. AU - Moraru, I. I. AU - Nickerson, D. AU - Sahle, S. AU - Snoep, J. L. PY - 2011 DA - 2011// TI - Reproducible computational biology experiments with sed-ml-the simulation experiment description markup language JO - BMC Syst Biol VL - 5 UR - https://doi.org/10.1186/1752-0509-5-198 DO - 10.1186/1752-0509-5-198 ID - Waltemath2011 ER - TY - STD TI - The R Project. https://www.r-project.org/. Accessed 5 Apr 2017. UR - https://www.r-project.org/ ID - ref39 ER - TY - JOUR AU - StataCorp, L. PY - 2007 DA - 2007// TI - Stata data analysis and statistical software JO - Spec Ed Release VL - 10 ID - StataCorp2007 ER - TY - STD TI - The Python Programming Language. http://www.python.org. Accessed 5 Apr 2017. UR - http://www.python.org ID - ref41 ER - TY - STD TI - The Java Programming Language. http://www.java.com. Accessed 5 Apr 2017. UR - http://www.java.com ID - ref42 ER - TY - JOUR AU - Wilson, G. PY - 2006 DA - 2006// TI - Software carpentry: getting scientists to write better code by making them more productive JO - Comput Sci Eng VL - 8 UR - https://doi.org/10.1109/MCSE.2006.122 DO - 10.1109/MCSE.2006.122 ID - Wilson2006 ER - TY - JOUR AU - Parnas, D. L. PY - 1972 DA - 1972// TI - On the criteria to be used in decomposing systems into modules JO - Commun ACM VL - 15 UR - https://doi.org/10.1145/361598.361623 DO - 10.1145/361598.361623 ID - Parnas1972 ER - TY - JOUR AU - Stefik, M. AU - Bobrow, D. G. PY - 1985 DA - 1985// TI - Object-oriented programming: Themes and variations JO - AI Mag VL - 6 ID - Stefik1985 ER - TY - JOUR AU - Meyer, B. PY - 1992 DA - 1992// TI - Applying’design by contract’ JO - Computer VL - 25 UR - https://doi.org/10.1109/2.161279 DO - 10.1109/2.161279 ID - Meyer1992 ER - TY - JOUR AU - Medvidovic, N. AU - Rosenblum, D. S. AU - Redmiles, D. F. AU - Robbins, J. E. PY - 2002 DA - 2002// TI - Modeling software architectures in the unified modeling language JO - ACM Trans Softw Eng Methodol (TOSEM) VL - 11 UR - https://doi.org/10.1145/504087.504088 DO - 10.1145/504087.504088 ID - Medvidovic2002 ER - TY - JOUR AU - Janzen, D. AU - Saiedian, H. PY - 2005 DA - 2005// TI - Test-driven development concepts, taxonomy, and future direction JO - Computer VL - 38 UR - https://doi.org/10.1109/MC.2005.314 DO - 10.1109/MC.2005.314 ID - Janzen2005 ER - TY - JOUR AU - Fucci, D. AU - Turhan, B. AU - Juristo, N. AU - Dieste, O. AU - Tosun-Misirli, A. AU - Oivo, M. PY - 2015 DA - 2015// TI - Towards an operationalization of test-driven development skills: An industrial empirical study JO - Inf Softw Technol VL - 68 UR - https://doi.org/10.1016/j.infsof.2015.08.004 DO - 10.1016/j.infsof.2015.08.004 ID - Fucci2015 ER - TY - STD TI - The SAS Analytical Software. https://www.sas.com/. Accessed 5 Apr 2017. UR - https://www.sas.com/ ID - ref50 ER - TY - STD TI - FUTS SAS Testing Library. https://info.thotwave.com/access-the-futs-framework-for-unit-testing-sas. Accessed 5 Apr 2017. UR - https://info.thotwave.com/access-the-futs-framework-for-unit-testing-sas ID - ref51 ER - TY - STD TI - SASUnit SAS Testing Library. https://sourceforge.net/projects/sasunit/. Accessed 5 Apr 2017. UR - https://sourceforge.net/projects/sasunit/ ID - ref52 ER - TY - JOUR AU - Wickham, H. PY - 2011 DA - 2011// TI - testthat: Get started with testing JO - R J VL - 3 ID - Wickham2011 ER - TY - STD TI - Burger M, Juenemann K, Koenig T. Runit: r unit test framework. R package version. 2009:0.4. https://cran.rstudio.com/web/packages/RUnit/. UR - https://cran.rstudio.com/web/packages/RUnit/ ID - ref54 ER - TY - STD TI - Grosjean P, Grosjean MP. Package ‘svunit’. 2013. https://cran.r-project.org/web/packages/svUnit/index.html. UR - https://cran.r-project.org/web/packages/svUnit/index.html ID - ref55 ER - TY - STD TI - Cheon Y, Leavens GT. A simple and practical approach to unit testing: The JML and JUnit way, vol. 2374. In: ECOOP. Springer: 2002. p. 231–55. ID - ref56 ER - TY - JOUR AU - Beaulieu-Jones, B. K. AU - Greene, C. S. PY - 2017 DA - 2017// TI - Reproducibility of computational workflows is automated using continuous analysis JO - Nat Biotechnol VL - 35 UR - https://doi.org/10.1038/nbt.3780 DO - 10.1038/nbt.3780 ID - Beaulieu-Jones2017 ER - TY - JOUR AU - Clarke, E. M. AU - Wing, J. M. PY - 1996 DA - 1996// TI - Formal methods: State of the art and future directions JO - ACM Comput Surv (CSUR) VL - 28 UR - https://doi.org/10.1145/242223.242257 DO - 10.1145/242223.242257 ID - Clarke1996 ER - TY - STD TI - Git Version Control System. https://git-scm.com/. Accessed 5 Apr 2017. UR - https://git-scm.com/ ID - ref59 ER - TY - STD TI - Subversion Version Control System. http://subversion.apache.org. Accessed 5 Apr 2017. UR - http://subversion.apache.org ID - ref60 ER - TY - JOUR AU - Pitt-Francis, J. AU - Bernabeu, M. O. AU - Cooper, J. AU - Garny, A. AU - Momtahan, L. AU - Osborne, J. AU - Pathmanathan, P. AU - Rodriguez, B. AU - Whiteley, J. P. AU - Gavaghan, D. J. PY - 2008 DA - 2008// TI - Chaste: using agile programming techniques to develop computational biology software JO - Philos Trans R Soc Lond A: Math, Phys Eng Sci VL - 366 UR - https://doi.org/10.1098/rsta.2008.0096 DO - 10.1098/rsta.2008.0096 ID - Pitt-Francis2008 ER - TY - STD TI - Papez V, Denaxas S. Evaluation of semantic web technologies for storing computable definitions of electronic health records phenotyping algorithms. Am Med Informa Assoc Annual Symp. 2017. https://arxiv.org/abs/1707.07673. UR - https://arxiv.org/abs/1707.07673 ID - ref62 ER - TY - STD TI - The CALIBER Data Portal. https://www.caliberresearch.org/portal/. Accessed 5 Apr 2017. UR - https://www.caliberresearch.org/portal/ ID - ref63 ER - TY - JOUR AU - Prlić, A. AU - Procter, J. B. PY - 2012 DA - 2012// TI - Ten simple rules for the open development of scientific software JO - PLoS Comput Biol VL - 8 UR - https://doi.org/10.1371/journal.pcbi.1002802 DO - 10.1371/journal.pcbi.1002802 ID - Prlić2012 ER - TY - JOUR AU - List, M. AU - Ebert, P. AU - Albrecht, F. PY - 2017 DA - 2017// TI - Ten simple rules for developing usable software in computational biology JO - PLoS Comput Biol VL - 13 UR - https://doi.org/10.1371/journal.pcbi.1005265 DO - 10.1371/journal.pcbi.1005265 ID - List2017 ER - TY - JOUR AU - Cock, P. J. AU - Antao, T. AU - Chang, J. T. AU - Chapman, B. A. AU - Cox, C. J. AU - Dalke, A. AU - Friedberg, I. AU - Hamelryck, T. AU - Kauff, F. AU - Wilczynski, B. PY - 2009 DA - 2009// TI - Biopython: freely available python tools for computational molecular biology and bioinformatics JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp163 DO - 10.1093/bioinformatics/btp163 ID - Cock2009 ER - TY - JOUR AU - Gentleman, R. C. AU - Carey, V. J. AU - Bates, D. M. AU - Bolstad, B. AU - Dettling, M. AU - Dudoit, S. AU - Ellis, B. AU - Gautier, L. AU - Ge, Y. AU - Gentry, J. PY - 2004 DA - 2004// TI - Bioconductor: open software development for computational biology and bioinformatics JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-10-r80 DO - 10.1186/gb-2004-5-10-r80 ID - Gentleman2004 ER - TY - JOUR AU - Springate, D. A. AU - Parisi, R. AU - Olier, I. AU - Reeves, D. AU - Kontopantelis, E. PY - 2017 DA - 2017// TI - rehr: An r package for manipulating and analysing electronic health record data JO - PloS ONE VL - 12 UR - https://doi.org/10.1371/journal.pone.0171784 DO - 10.1371/journal.pone.0171784 ID - Springate2017 ER - TY - JOUR AU - Giardine, B. AU - Riemer, C. AU - Hardison, R. C. AU - Burhans, R. AU - Elnitski, L. AU - Shah, P. AU - Zhang, Y. AU - Blankenberg, D. AU - Albert, I. AU - Taylor, J. PY - 2005 DA - 2005// TI - Galaxy: a platform for interactive large-scale genome analysis JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.4086505 DO - 10.1101/gr.4086505 ID - Giardine2005 ER - TY - JOUR AU - Wolstencroft, K. AU - Haines, R. AU - Fellows, D. AU - Williams, A. AU - Withers, D. AU - Owen, S. AU - Soiland-Reyes, S. AU - Dunlop, I. AU - Nenadic, A. AU - Fisher, P. PY - 2013 DA - 2013// TI - The taverna workflow suite: designing and executing workflows of web services on the desktop, web or in the cloud JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gkt328 DO - 10.1093/nar/gkt328 ID - Wolstencroft2013 ER - TY - JOUR AU - Köster, J. AU - Rahmann, S. PY - 2012 DA - 2012// TI - Snakemake—a scalable bioinformatics workflow engine JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts480 DO - 10.1093/bioinformatics/bts480 ID - Köster2012 ER - TY - JOUR AU - de la Garza, L. AU - Veit, J. AU - Szolek, A. AU - Röttig, M. AU - Aiche, S. AU - Gesing, S. AU - Reinert, K. AU - Kohlbacher, O. PY - 2016 DA - 2016// TI - From the desktop to the grid: scalable bioinformatics via workflow conversion JO - BMC Bioinforma VL - 17 UR - https://doi.org/10.1186/s12859-016-0978-9 DO - 10.1186/s12859-016-0978-9 ID - de la Garza2016 ER - TY - JOUR AU - Fink, J. PY - 2014 DA - 2014// TI - Docker: a software as a service, operating system-level virtualization framework JO - Code4Lib J VL - 25 ID - Fink2014 ER - TY - STD TI - Conda.io. https://conda.io/. Accessed 5 Apr 2017. UR - https://conda.io/ ID - ref74 ER - TY - JOUR AU - Guide, M. U. PY - 1998 DA - 1998// TI - The mathworks inc JO - Natick MA VL - 4 ID - Guide1998 ER - TY - STD TI - The Octave Analytical Software. https://www.gnu.org/software/octave/. Accessed 5 Apr 2017. UR - https://www.gnu.org/software/octave/ ID - ref76 ER - TY - JOUR AU - Hurley, D. G. AU - Budden, D. M. AU - Crampin, E. J. PY - 2015 DA - 2015// TI - Virtual reference environments: a simple way to make research reproducible JO - Brief Bioinform VL - 16 UR - https://doi.org/10.1093/bib/bbu043 DO - 10.1093/bib/bbu043 ID - Hurley2015 ER - TY - STD TI - Oracle VirtualBox Virtualization Software. https://www.virtualbox.org. Accessed 5 Apr 2017. UR - https://www.virtualbox.org ID - ref78 ER - TY - STD TI - VMware Virtualization Software. http://www.vmware.com/. Accessed 5 Apr 2017. UR - http://www.vmware.com/ ID - ref79 ER - TY - JOUR AU - Mo, H. AU - Thompson, W. K. AU - Rasmussen, L. V. AU - Pacheco, J. A. AU - Jiang, G. AU - Kiefer, R. AU - Zhu, Q. AU - Xu, J. AU - Montague, E. AU - Carrell, D. S. PY - 2015 DA - 2015// TI - Desiderata for computable representations of electronic health records-driven phenotype algorithms JO - J Am Med Inform Assoc VL - 22 ID - Mo2015 ER - TY - STD TI - Pathak J, Kiefer RC, Bielinski SJ, Chute CG. Applying semantic web technologies for phenome-wide scan using an electronic health record linked Biobank. J Biomed Semant. 2012; 3(1):10. doi:10.1186/2041-1480-3-10. https://doi.org/10.1186/2041-1480-3-10. UR - https://doi.org/10.1186/2041-1480-3-10 ID - ref81 ER - TY - STD TI - Figshare. https://figshare.com/. Accessed 5 Apr 2017. UR - https://figshare.com/ ID - ref82 ER - TY - STD TI - The Journal of Open Source Software. http://joss.theoj.org/. Accessed 5 Apr 2017. UR - http://joss.theoj.org/ ID - ref83 ER - TY - JOUR AU - Knuth, D. E. PY - 1984 DA - 1984// TI - Literate programming JO - The Computer Journal VL - 27 UR - https://doi.org/10.1093/comjnl/27.2.97 DO - 10.1093/comjnl/27.2.97 ID - Knuth1984 ER - TY - STD TI - Roxygen Package. https://cran.r-project.org/web/packages/roxygen2/index.html. Accessed 5 July 2017. UR - https://cran.r-project.org/web/packages/roxygen2/index.html ID - ref85 ER - TY - BOOK AU - Xie, Y. PY - 2015 DA - 2015// TI - Dynamic Documents with R and Knitr, vol 29. PB - CRC Press CY - Florida ID - Xie2015 ER - TY - STD TI - Leisch F. Sweave: Dynamic generation of statistical reports using literate data analysis. In: Compstat. Springer: 2002. p. 575–80. http://www.springer.com/us/book/9783790815177. UR - http://www.springer.com/us/book/9783790815177 ID - ref87 ER - TY - STD TI - Ragan-Kelley M, Perez F, Granger B, Kluyver T, Ivanov P, Frederic J, Bussonier M. The jupyter/ipython architecture: a unified view of computational research, from interactive exploration to communication and publication. In: AGU Fall Meeting Abstracts.2014. p. 07. http://adsabs.harvard.edu/abs/2014AGUFM.H44D..07R. UR - http://adsabs.harvard.edu/abs/2014AGUFM.H44D..07R ID - ref88 ER - TY - STD TI - MIMIC-III Source Code Repository. https://github.com/MIT-LCP/mimic-code. Accessed 5 Apr 2017. UR - https://github.com/MIT-LCP/mimic-code ID - ref89 ER - TY - STD TI - Johnson AEW, Pollard TJ, Shen L, Lehman L-wH, Feng M, Ghassemi M, Moody B, Szolovits P, Celi LA, Mark RG. MIMIC-III, a freely accessible critical care database. Sci Data. 2016; 3. Nature Publishing Group. ID - ref90 ER - TY - JOUR AU - Aboab, J. AU - Celi, L. A. AU - Charlton, P. AU - Feng, M. AU - Ghassemi, M. AU - Marshall, D. C. AU - Mayaud, L. AU - Naumann, T. AU - McCague, N. AU - Paik, K. E. PY - 2016 DA - 2016// TI - A “datathon” model to support cross-disciplinary collaboration JO - Sci Transl Med VL - 8 UR - https://doi.org/10.1126/scitranslmed.aad9072 DO - 10.1126/scitranslmed.aad9072 ID - Aboab2016 ER - TY - JOUR AU - Gentleman, R. AU - Temple Lang, D. PY - 2007 DA - 2007// TI - Statistical analyses and reproducible research JO - J Comput Graph Stat VL - 16 UR - https://doi.org/10.1198/106186007X178663 DO - 10.1198/106186007X178663 ID - Gentleman2007 ER - TY - JOUR AU - Peng, R. D. AU - Dominici, F. AU - Pastor-Barriuso, R. AU - Zeger, S. L. AU - Samet, J. M. PY - 2005 DA - 2005// TI - Seasonal analyses of air pollution and mortality in 100 us cities JO - Am J Epidemiol VL - 161 UR - https://doi.org/10.1093/aje/kwi075 DO - 10.1093/aje/kwi075 ID - Peng2005 ER - TY - JOUR AU - Ioannidis, J. P. PY - 2005 DA - 2005// TI - Why most published research findings are false JO - PLos med VL - 2 UR - https://doi.org/10.1371/journal.pmed.0020124 DO - 10.1371/journal.pmed.0020124 ID - Ioannidis2005 ER - TY - STD TI - Version Control. https://en.wikipedia.org/wiki/Version_Control. Accessed 28 July 2017. UR - https://en.wikipedia.org/wiki/Version_Control ID - ref95 ER - TY - STD TI - Doxygen. http://doxygen.org/. Accessed 5 Apr 2017. UR - http://doxygen.org/ ID - ref96 ER - TY - JOUR AU - Lenth, R. V. AU - Højsgaard, S. PY - 2007 DA - 2007// TI - Sasweave: Literate programming using sas JO - J Stat Softw VL - 19 UR - https://doi.org/10.18637/jss.v019.i08 DO - 10.18637/jss.v019.i08 ID - Lenth2007 ER -