bibliography.bib

@article{verma2013lack,
  title={Lack of Software Engineering Practices in the Development of Bioinformatics Software},
  author={Verma, Dhawal and Gesell, Jon and Siy, Harvey and Zand, Mansour},
  booktitle={ICCGI 2013, The Eighth International Multi-Conference on Computing in the Global Information Technology},
  pages={57--62},
  year={2013}
},

@article{prabhu2011survey,
  title={A survey of the practice of computational science},
  author={Prabhu, Prakash and Jablin, Thomas B and Raman, Arun and Zhang, Yun and Huang, Jialu and Kim, Hanjun and Johnson, Nick P and Liu, Feng and Ghosh, Soumyadeep and Beard, Stephen and others},
  booktitle={State of the Practice Reports},
  pages={19},
  year={2011},
  organization={ACM}
},

@article{wilson2014best,
  title={Best practices for scientific computing},
  author={Wilson, Greg and Aruliah, DA and Brown, C Titus and Hong, Neil P Chue and Davis, Matt and Guy, Richard T and Haddock, Steven HD and Huff, Kathryn D and Mitchell, Ian M and Plumbley, Mark D and others},
  journal={PLoS biology},
  volume={12},
  number={1},
  pages={e1001745},
  year={2014},
  publisher={Public Library of Science}
},

@article{baxter2006scientific,
  title={Scientific software development is not an oxymoron},
  author={Baxter, Susan M and Day, Steven W and Fetrow, Jacquelyn S and Reisinger, Stephanie J},
  journal={PLoS computational biology},
  volume={2},
  number={9},
  pages={e87},
  year={2006},
  publisher={Public Library of Science}
},

@article{segal2008developing,
  title={Developing scientific software},
  author={Segal, Judith and Morris, Chris},
  journal={Software, IEEE},
  volume={25},
  number={4},
  pages={18--20},
  year={2008},
  publisher={IEEE}
},

@article{sanders2008dealing,
  title={Dealing with risk in scientific software development},
  author={Sanders, Rebecca and Kelly, Diane},
  journal={IEEE software},
  volume={25},
  number={4},
  pages={21--28},
  year={2008},
  publisher={[Los Alamitos, CA: IEEE Computer Society, c1984-}
},

@book{dijkstra1982selected,
  title={Selected writings on computing: a personal perspective},
  author={Dijkstra, Edsger W},
  year={1982},
  publisher={Springer-Verlag New York, Inc.}
},
@article{bennett2009principled,
  title={The principled control of false positives in neuroimaging},
  author={Bennett, Craig M and Wolford, George L and Miller, Michael B},
  journal={Social cognitive and affective neuroscience},
  volume={4},
  number={4},
  pages={417--422},
  year={2009},
  publisher={Oxford University Press}
},

@article{ioannidis2005most,
  title={Why most published research findings are false},
  author={Ioannidis, John PA},
  journal={PLoS medicine},
  volume={2},
  number={8},
  pages={e124},
  year={2005},
  publisher={Public Library of Science}
},

@article{cockburn1999characterizing,
  title={Characterizing people as non-linear, first-order components in software development},
  author={Cockburn, Alistair},
  booktitle={International Conference on Software Engineering 2000},
  year={1999}
},

@article{umarji2009software,
  title={Software engineering education for bioinformatics},
  author={Umarji, Medha and Seaman, Carolyn and Koru, Akif G{\"u}nes and Liu, Hongfang},
  booktitle={Software Engineering Education and Training, 2009. CSEET'09. 22nd Conference on},
  pages={216--223},
  year={2009},
  organization={IEEE}
},
@article{hannay2009scientists,
  title={How do scientists develop and use scientific software?},
  author={Hannay, Jo Erskine and MacLeod, Carolyn and Singer, Janice and Langtangen, Hans Petter and Pfahl, Dietmar and Wilson, Greg},
  booktitle={Proceedings of the 2009 ICSE workshop on Software Engineering for Computational Science and Engineering},
  pages={1--8},
  year={2009},
  organization={IEEE Computer Society}
},
@article{segal2004professional,
  title={Professional end user developers and software development knowledge},
  author={Segal, Judith},
  journal={Department of Computing, Open University, Milton Keynes, MK7 6AA, UK, Tech. Rep},
  year={2004},
  publisher={Citeseer}
},
@article{segal2007some,
  title={Some problems of professional end user developers},
  author={Segal, Judith},
  booktitle={Visual Languages and Human-Centric Computing, 2007. VL/HCC 2007. IEEE Symposium on},
  pages={111--118},
  year={2007},
  organization={IEEE}
},
@article{nguyen2010survey,
  title={A survey of scientific software development},
  author={Nguyen-Hoan, Luke and Flint, Shayne and Sankaranarayana, Ramesh},
  booktitle={Proceedings of the 2010 ACM-IEEE International Symposium on Empirical Software Engineering and Measurement},
  pages={12},
  year={2010},
  organization={ACM}
},

@article{surendran2002simulating,
  title={Simulating a software engineering apprenticeship},
  author={Surendran, Ken and Hays, Helen and Macfarlane, Andrew},
  journal={Software, IEEE},
  volume={19},
  number={5},
  pages={49--56},
  year={2002},
  publisher={IEEE}
},
@article{morris2008some,
  title={Some lessons learned reviewing scientific code},
  author={Morris, Chris},
  booktitle={Proceedings of the 30th International Conference on Software Engineering (ICSE08)},
  year={2008}
},
@article{chilana2009comparing,
  title={Comparing bioinformatics software development by computer scientists and biologists: An exploratory study},
  author={Chilana, Parmit K and Palmer, Carole L and Ko, Andrew J},
  booktitle={Software Engineering for Computational Science and Engineering, 2009. SECSE'09. ICSE Workshop on},
  pages={72--79},
  year={2009},
  organization={IEEE}
},
@article{letondal2004participatory,
  title={Participatory programming and the scope of mutual responsibility: balancing scientific, design and software commitment},
  author={Letondal, Catherine and Mackay, Wendy E},
  booktitle={Proceedings of the eighth conference on Participatory design: Artful integration: interweaving media, materials and practices-Volume 1},
  pages={31--41},
  year={2004},
  organization={ACM}
},
@article{segal2005software,
  title={When software engineers met research scientists: A case study},
  author={Segal, Judith},
  journal={Empirical Software Engineering},
  volume={10},
  number={4},
  pages={517--536},
  year={2005},
  publisher={Springer}
},
@article{elliott2012epistemic,
  title={Epistemic and methodological iteration in scientific research},
  author={Elliott, Kevin C},
  journal={Studies in History and Philosophy of Science Part A},
  volume={43},
  number={2},
  pages={376--382},
  year={2012},
  publisher={Elsevier}
},
@article{swertz2007beyond,
  title={Beyond standardization: dynamic software infrastructures for systems biology},
  author={Swertz, Morris A and Jansen, Ritsert C},
  journal={Nature Reviews Genetics},
  volume={8},
  number={3},
  pages={235--243},
  year={2007},
  publisher={Nature Publishing Group}
},
@article{kosar2008preliminary,
  title={A preliminary study on various implementation approaches of domain-specific language},
  author={Kosar, Toma{\v{z}} and Barrientos, Pablo A and Mernik, Marjan and others},
  journal={Information and Software Technology},
  volume={50},
  number={5},
  pages={390--405},
  year={2008},
  publisher={Elsevier}
},
@article{van2000domain,
  title={Domain-Specific Languages: An Annotated Bibliography.},
  author={Van Deursen, Arie and Klint, Paul and Visser, Joost},
  journal={Sigplan Notices},
  volume={35},
  number={6},
  pages={26--36},
  year={2000}
},
@article{kane2006agile,
  title={Agile methods in biomedical software development: a multi-site experience report},
  author={Kane, David W and Hohman, Moses M and Cerami, Ethan G and McCormick, Michael W and Kuhlmman, Karl F and Byrd, Jeff A},
  journal={Bmc Bioinformatics},
  volume={7},
  number={1},
  pages={273},
  year={2006},
  publisher={BioMed Central Ltd}
},
@article{ruffin2002david,
  title={David Ricardo's discovery of comparative advantage},
  author={Ruffin, Roy},
  journal={History of Political Economy},
  volume={34},
  number={4},
  pages={727--748},
  year={2002},
  publisher={Duke University Press}
},
@article{walsh2013accelerating,
  title={Accelerating in silico research with workflows: a lesson in simplicity},
  author={Walsh, Paul and Carroll, John and Sleator, Roy D},
  journal={Computers in biology and medicine},
  volume={43},
  number={12},
  pages={2028--2035},
  year={2013},
  publisher={Elsevier}
},
@article{szigeti2014openworm,
  title={OpenWorm: an open-science approach to modeling Caenorhabditis elegans},
  author={Szigeti, Bal{\'a}zs and Gleeson, Padraig and Vella, Michael and Khayrulin, Sergey and Palyanov, Andrey and Hokanson, Jim and Currie, Michael and Cantarelli, Matteo and Idili, Giovanni and Larson, Stephen},
  journal={Frontiers in computational neuroscience},
  volume={8},
  year={2014},
  publisher={Frontiers Media SA}
},
@article{idili2011managing,
  title={Managing complexity in multi-algorithm, multi-scale biological simulations: an integrated software engineering and neuroinformatics approach},
  author={Idili, Giovanni and Cantarelli, Matteo and Buibas, Marius and Busbice, Tim and Coggan, Jay and Grove, Christian and Khayrulin, Sergey and Palyanov, Andrey and Larson, Stephen D},
  booktitle={Frontiers in Neuroinformatics Conference Abstract: 4th INCF Congress of Neuroinformatics},
  volume={112},
  year={2011}
},
@inproceedings{schindewolf2012scientific,
  title={What scientific applications can benefit from hardware transactional memory?},
  author={Schindewolf, Martin and Biliari, Barna and Gyllenhaal, John and Schulz, Martin and Wang, Amy and Karl, Wolfgang},
  booktitle={High Performance Computing, Networking, Storage and Analysis (SC), 2012 International Conference for},
  pages={1--11},
  year={2012},
  organization={IEEE}
},
@article{agha1997foundation,
  title={A foundation for actor computation},
  author={Agha, Gul A and Mason, Ian A and Smith, Scott F and Talcott, Carolyn L},
  journal={Journal of Functional Programming},
  volume={7},
  number={01},
  pages={1--72},
  year={1997},
  publisher={Cambridge Univ Press}
},
@article{wiewiorka2014sparkseq,
  title={SparkSeq: fast, scalable, cloud-ready tool for the interactive genomic data analysis with nucleotide precision},
  author={Wiewi{\'o}rka, Marek S and Messina, Antonio and Pacholewska, Alicja and Maffioletti, Sergio and Gawrysiak, Piotr and Okoniewski, Micha{\l} J},
  journal={Bioinformatics},
  pages={btu343},
  year={2014},
  publisher={Oxford Univ Press}
}