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The 2015 Bioinformatics Open Source Conference (BOSC 2015)

Nomi L. Harris, Peter J. A. Cock, Hilmar Lapp, Brad Chapman, Rob Davey, Christopher Fields, Karsten Hokamp, Monica Munoz-Torres
2016 PLoS Computational Biology  
The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development  ...  BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference.  ...  In particular, we are grateful to Google for their generous support for video recording BOSC 2015, and to our returning sponsors Curoverse (the team behind the open source platform Arvados) and GigaScience  ... 
doi:10.1371/journal.pcbi.1004691 pmid:26914653 pmcid:PMC4767331 fatcat:tveqo2l6krbxtfxhdu4k6t7o6e

The Bioinformatics Open Source Conference (BOSC) 2013

N. L. Harris, P. J. A. Cock, B. A. Chapman, J. Goecks, H.-R. Hotz, H. Lapp
2014 Bioinformatics  
The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development  ...  BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference.  ...  In particular, we are grateful to Google for their generous support for video recording BOSC 2015, and to our returning sponsors Curoverse (the team behind the open source platform Arvados) and GigaScience  ... 
doi:10.1093/bioinformatics/btu413 pmid:25024288 pmcid:PMC4287938 fatcat:bms4n2qavjfkjjjy6kob33dgny

Message from the ISCB: ISMB/ECCB Rebooted: 2015 Brings Major Update to the Conference Program

C. N. Fogg, D. E. Kovats
2015 Bioinformatics  
ECCB 2015) is shaping up to be a phenomenal meeting with world-renowned keynote speakers and changes in the conference format that aim to make for a more streamlined and user-friendly conference.  ...  As in the past, submissions accepted into the highly selective Proceedings track will be published in a special ISMB/ECCB Proceedings issue of Bioinformatics.  ...  ) Bio-Ontologies BioVis SIG BOSC: The 16th Annual Bioinformatics Open Source Conference HitSEQ: High Throughput Sequencing Algorithms and Applications Integrative RNA Biology SIG NetBio SIG Regulatory  ... 
doi:10.1093/bioinformatics/btv207 fatcat:4xzirvkitbatbknlndzgv3xede

Anatomy of BioJS, an open source community for the life sciences

Guy Yachdav, Tatyana Goldberg, Sebastian Wilzbach, David Dao, Iris Shih, Saket Choudhary, Steve Crouch, Max Franz, Alexander García, Leyla J García, Björn A Grüning, Devasena Inupakutika (+9 others)
2015 eLife  
The lessons we have learned on BioJS may also be relevant to other open source software projects.  ...  BioJS is an open source software project that develops visualization tools for different types of biological data.  ...  Acknowledgements We thank Henning Hermjakob and Rafael Jimenez, who founded and supported BioJS through its early days, and John G ómez, who developed the first release of the BioJS library.  ... 
doi:10.7554/elife.07009 pmid:26153621 pmcid:PMC4495654 fatcat:7dwu6xkfk5gzdp44olw3ti3foe

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols

Alexandros Kanterakis, Joël Kuiper, George Potamias, Morris A. Swertz
2015 Source Code for Biology and Medicine  
Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science.  ...  However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols.  ...  Funding The research leading to these results has received funding from the Ubbo Emmius Fund to AK, the European Union Seventh Framework Programme  ... 
doi:10.1186/s13029-015-0042-6 pmid:26587054 pmcid:PMC4652372 fatcat:tw7dzq6jazc37l4nqy7gzmd7aq

Computational Biology: Moving into the Future One Click at a Time

Christiana N. Fogg, Diane E. Kovats
2015 PLoS Computational Biology  
Lynn Fink and Mark Gerstein in 2008, titled "Open Access: Taking Full Advantage of the Content," which argued that the full potential of open access has not been realized, as "no killer apps" exist that  ...  Bourne also developed the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) and Immune Epitope Database (IEDB), which have become valuable data resources for the research  ...  Indeed, it was the culture of open source software supported by ISCB, especially members of the Bioinformatics Open Source Conference (BOSC) community, which drew Markel to the Society.  ... 
doi:10.1371/journal.pcbi.1004323 pmid:26107876 pmcid:PMC4481313 fatcat:v42d6pobgbfrxjr7oxo67hm2v4

Efforts Towards Accessible And Reliable Bioinformatics

Matúš Kalaš, Inge Jonassen
2015 Zenodo  
As diverse components are necessary for the accessible and reliable bioinformatics scenario, our work focussed in particular on the following: In the BioXSD project, we aimed at developing an XML-Schema-based  ...  The EDAM ontology aimed at enumerating and organising concepts within bioinformatics, including operations and types of data.  ...  O|B|F supports and promotes free/open-source software within bioinformatics, and organises an annual Bioinformatics Open Source Conference (BOSC, Harris et al. 2015) and various "hackathons" gathering  ... 
doi:10.5281/zenodo.33715 fatcat:2pxqpqu5yvat3ctdedqam3sjsi

How to Hackathon: Socio-technical Tradeoffs in Brief, Intensive Collocation

Erik H. Trainer, Arun Kalyanasundaram, Chalalai Chaihirunkarn, James D. Herbsleb
2016 Proceedings of the 19th ACM Conference on Computer-Supported Cooperative Work & Social Computing - CSCW '16  
Do the activities participants select suggest a tradeoff between the social and technical benefits of collocation?  ...  We present results from a multiple-case study that suggest the way that hackathon-style collocation advances technical work varies across technical domain, community structure, and expertise of participants  ...  Sloan Foundation, the National Evolutionary Synthesis Center (NESCent), NESCent's National Science Foundation award EF-0905606, and the Google Open Source Programs Office.  ... 
doi:10.1145/2818048.2819946 dblp:conf/cscw/TrainerKCH16 fatcat:fyb7ic6fpnhcxm4egkiioz33g4

A Systematic Literature Review for Implementing Data Ops in the Data Warehouse Lifecycle during the ETL Phase

Ahmed Bahaa, Sherif Ragab Eldemerdash, Hanan Fahmy
2021 Journal of Computer Science  
The expected results of this study may be articles in open-source journals (arXiv journal and reduced Cantered on the following variables: CEUR-WS  ...  satisfied our across data sources.  ... 
doi:10.3844/jcssp.2021.1011.1030 fatcat:zfmfb3uvpnaqpe3c6ghgshaxye

D5.1 Interoperability Implementation Regulations

Carol Goble, Chris Evelo, Helen Parkinson, ELIXIR Interoperability Community
2018 Zenodo  
During the execution of EXCELERATE we have significantly refined and adapted this vision to offer a flexible and practical open framework for developing and deploying interoperability across the WPs, working  ...  The main aim of this deliverable is to present our progress for the implementation of our interoperability framework for EXCELERATE Use Cases WP6-9 and the ELIXIR Data Platform (WP3).  ...  It is overseen by the Open API Initiative, an open source collaborative project of the Linux Foundation.  ... 
doi:10.5281/zenodo.1452414 fatcat:j6bod5nlinadhl623uez7x46m4

Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv

Farah Zaib Khan, Stian Soiland-Reyes, Richard O. Sinnott, Andrew Lonie, Carole Goble, Michael R. Crusoe
2018 Zenodo  
We utilise open source community-driven standards; interoperable workflow definitions in Common Workflow Language (CWL), structured provenance representation using the W3C PROV model, and resource aggregation  ...  The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research.  ...  We are grateful for partial travel support from Open Bioinformatics Foundation (OBF) Travel Fellowship Program [150] to Farah Zaib Khan for attending the Bioinformatics Open Source Conference (BOSC)  ... 
doi:10.5281/zenodo.1966881 fatcat:gnpjnqu6pzdtfe7d4nzvi2r44a

Marine Turtle Newsletter

Francis R. Cook
2009 Canadian field-naturalist  
of about 600 m (Bosc & Le Gall 1986) .  ...  The status of marine turtles in the Mediterranean. In: Margaritoulis, D. & A. Demetropoulos (Eds.). Proceedings of the First Mediterranean Conference on Marine Turtles.  ...  Aim The Marine Turtle Newsletter (MTN) provides current information on marine turtle research, biology, conservation and status, in an open-access format.  ... 
doi:10.22621/cfn.v123i3.978 fatcat:wvadw6v4yrakljiivtnb7tt2qa

Marine Turtle Newsletter

Francis R. Cook
2008 Canadian field-naturalist  
of about 600 m (Bosc & Le Gall 1986) .  ...  The status of marine turtles in the Mediterranean. In: Margaritoulis, D. & A. Demetropoulos (Eds.). Proceedings of the First Mediterranean Conference on Marine Turtles.  ...  Aim The Marine Turtle Newsletter (MTN) provides current information on marine turtle research, biology, conservation and status, in an open-access format.  ... 
doi:10.22621/cfn.v122i3.617 fatcat:5tdobyiepnc5hjlwozvvudcys4

Marine Turtle Newsletter

Francis Cook
2007 Canadian field-naturalist  
of about 600 m (Bosc & Le Gall 1986) .  ...  The status of marine turtles in the Mediterranean. In: Margaritoulis, D. & A. Demetropoulos (Eds.). Proceedings of the First Mediterranean Conference on Marine Turtles.  ...  Aim The Marine Turtle Newsletter (MTN) provides current information on marine turtle research, biology, conservation and status, in an open-access format.  ... 
doi:10.22621/cfn.v121i1.404 fatcat:t7oa72kw7natzkhmehgcwrh5ly

Marine Turtle Newsletter

Francis R. Cook
2009 Canadian field-naturalist  
of about 600 m (Bosc & Le Gall 1986) .  ...  The status of marine turtles in the Mediterranean. In: Margaritoulis, D. & A. Demetropoulos (Eds.). Proceedings of the First Mediterranean Conference on Marine Turtles.  ...  Aim The Marine Turtle Newsletter (MTN) provides current information on marine turtle research, biology, conservation and status, in an open-access format.  ... 
doi:10.22621/cfn.v123i2.934 fatcat:2g2lrtembja4ti6sradhb7jlxq
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