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bcbio-nextgen: Automated, distributed next-gen sequencing pipeline

Roman Valls Guimera
2012 EMBnet journal  
doi:10.14806/ej.17.b.286 fatcat:z7q7gszu55hblof3dr5l5u3fjy

Fastphylo: Fast tools for phylogenetics

Mehmood Khan, Isaac Elias, Erik Sjölund, Kristina Nylander, Roman Guimera, Richard Schobesberger, Peter Schmitzberger, Jens Lagergren, Lars Arvestad
2013 BMC Bioinformatics  
Distance methods are ubiquitous tools in phylogenetics. Their primary purpose may be to reconstruct evolutionary history, but they are also used as components in bioinformatic pipelines. However, poor computational efficiency has been a constraint on the applicability of distance methods on very large problem instances. Results: We present fastphylo, a software package containing implementations of efficient algorithms for two common problems in phylogenetics: estimating DNA/protein sequence
more » ... tances and reconstructing a phylogeny from a distance matrix. We compare fastphylo with other neighbor joining based methods and report the results in terms of speed and memory efficiency. Conclusions: Fastphylo is a fast, memory efficient, and easy to use software suite. Due to its modular architecture, fastphylo is a flexible tool for many phylogenetic studies. Implementation Fastphylo consists of four modules: fastdist, fastprot, fastprot_mpi, and fnj. All these modules are implemented in C++ (compiled with GCC v4.7) and have been verified to compile on popular
doi:10.1186/1471-2105-14-334 pmid:24255987 pmcid:PMC4225504 fatcat:47xbjep3anbm3nrnusse2quasm

Arteria: An automation system for a sequencing core facility

Johan Dahlberg, Johan Hermansson, Steinar Sturlaugsson, Mariya Lysenkova, Patrik Smeds, Claes Ladenvall, Roman Valls Guimera, Florian Reisinger, Oliver Hofmann, Pontus Larsson
2019 GigaScience  
Background In recent years, nucleotide sequencing has become increasingly instrumental in both research and clinical settings. This has led to an explosive growth in sequencing data produced worldwide. As the amount of data increases, so does the need for automated solutions for data processing and analysis. The concept of workflows has gained favour in the bioinformatics community, but there is little in the scientific literature describing end-to-end automation systems. Arteria is an
more » ... n system that aims at providing a solution to the data-related operational challenges that face sequencing core facilities. Findings Arteria is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. In this article we describe the system, elaborate on the underlying conceptual framework, and present an example implementation. Arteria can be reduced to 3 conceptual levels: orchestration (using an event-based model of automation), process (the steps involved in processing sequencing data, modelled as workflows), and execution (using a series of RESTful micro-services). This creates a system that is both flexible and scalable. Arteria-based systems have been successfully deployed at 3 sequencing core facilities. The Arteria Project code, written largely in Python, is available as open source software, and more information can be found at https://arteria-project.github.io/ . Conclusions We describe the Arteria system and the underlying conceptual framework, demonstrating how this model can be used to automate data handling and analysis in the context of a sequencing core facility.
doi:10.1093/gigascience/giz135 pmid:31825479 pmcid:PMC6905352 fatcat:g4z3pf7mg5genksv65rrdecigq

Introducing JOSS: The Journal of Open Source Software [article]

Arfon Smith, Lorena A. Barba, George Githinji, Melissa Gymrek, Kathryn Huff, Daniel S. Katz, Christopher Madan, Abigail Cabunoc Mayes, Kevin M Moerman, Kyle Niemeyer, Pjotr Prins, Karthik Ram (+4 others)
2017 Figshare  
Talk presented at the 2017 Python in Science Conference (SciPy), on 13 July 2017 in Austin, TX.AbstractThis talk describes the motivation and progress of the Journal of Open Source Software (JOSS), a free, open-access journal designed to publish brief articles about research software. The primary purpose of JOSS is to enable developers of research software to receive citation credit equivalent to typical archival publications. Rather than a review of a lengthy software paper (including, e.g.,
more » ... thodology, validation, sample results), JOSS submissions undergo rigorous peer review of both the abstract and software itself, including documentation, tests, continuous integration, and licensing. The JOSS review process is modeled on the established approach of the rOpenSci collaboration. The entire submission and review process occurs openly on GitHub; articles not yet accepted remain visible and under review until the authors make appropriate changes for acceptance—unlike other journals, articles requiring major revision are not rejected. JOSS published 111 articles in its first year (May 2016–2016), with >50 articles under review.
doi:10.6084/m9.figshare.5208151 fatcat:s3qlrvcylzhyvgx33mgjdi74vi

Sprints, Hackathons and Codefests as community gluons in computational biology

Steffen Möller, Enis Afgan, Michael Banck, Peter J. A. Cock, Matus Kalas, Laszlo Kajan, Pjotr Prins, Jacqueline Quinn, Olivier Sallou, Francesco Strozzi, Torsten Seemann, Andreas Tille (+3 others)
2013 EMBnet journal  
doi:10.14806/ej.19.b.726 fatcat:n7hmrivnpfekzgrdcj4f5tpndq

Experiences with workflows for automating data-intensive bioinformatics

Ola Spjuth, Erik Bongcam-Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimera, Aleksi Kallio, Eija Korpelainen, Maciej M Kańduła, Milko Krachunov, David P Kreil, Ognyan Kulev (+6 others)
2015 Biology Direct  
High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources and carry out data management and analysis tasks on large scale. Workflow systems can be useful to simplify construction of analysis pipelines that automate tasks, support reproducibility and provide measures for fault-tolerance. However, workflow systems can incur significant development and
more » ... nistration overhead so bioinformatics pipelines are often still built without them. We present the experiences with workflows and workflow systems within the bioinformatics community participating in a series of hackathons and workshops of the EU COST action SeqAhead. The organizations are working on similar problems, but we have addressed them with different strategies and solutions. This fragmentation of efforts is inefficient and leads to redundant and incompatible solutions. Based on our experiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics workflow construction and execution.
doi:10.1186/s13062-015-0071-8 pmid:26282399 pmcid:PMC4539931 fatcat:cxotvdjwrndblm7gvu5myegsrq

Community-driven development for computational biology at Sprints, Hackathons and Codefests

Steffen Möller, Enis Afgan, Michael Banck, Raoul JP Bonnal, Timothy Booth, John Chilton, Peter JA Cock, Markus Gumbel, Nomi Harris, Richard Holland, Matúš Kalaš, László Kaján (+16 others)
2014 BMC Bioinformatics  
Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by
more » ... formal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. Results: This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. Conclusions: Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.
doi:10.1186/1471-2105-15-s14-s7 pmid:25472764 pmcid:PMC4255748 fatcat:p7jbtuipnbdafo3zauaqrhu5sq

Journal of Open Source Software (JOSS): design and first-year review

Arfon M. Smith, Kyle E. Niemeyer, Daniel S. Katz, Lorena A. Barba, George Githinji, Melissa Gymrek, Kathryn D. Huff, Christopher R. Madan, Abigail Cabunoc Mayes, Kevin M. Moerman, Pjotr Prins, Karthik Ram (+4 others)
2018 PeerJ Computer Science  
They are George Githinji, Melissa Gymrek, Pjotr Prins, 43 Ariel Rokem, and Roman Valls Guimera.  ... 
doi:10.7717/peerj-cs.147 pmid:32704456 pmcid:PMC7340488 fatcat:groqd7oapre3nhxebxrsvunxgy

Page 324 of Chautauquan Vol. 55, Issue 3 [page]

1909 Chautauquan  
Roman architecture may be studied at Italica, Tarra- gona, Segovia, and Sagunto. Remains of Visgothic archi- tecture are scarce, but some of them may be seen at Cér- doba, Toledo, and Barcelona.  ...  Fiske, the American public was given the privilege of seeing “Marta of the Lowlands,” a very powerfui drama by Guimera; and this winter Mr. and Mrs.  ... 

El teatre musical d'Àngel Guimerà

Maridés Soler
2014 Revista de lenguas y literaturas catalana gallega y vasca  
Ja des dels inicis de la seva carrera com a dramaturg, Guimerà va procurar introduir música en les seves obres mantenint intensos contactes amb els principals compositors de l'època (Morera, Vives i Pahissa  ...  Already from beginning his career as playwriter, Guimerà always tried to introduce music in his plays and looked for close contact with the main composers of his time (Morera, Vives and Pahissa); firstly  ...  enamorat de la reina en la seva joventut, encara se'n 29 A La Miralta, després de la cerimònia nupcial del Carles i la Dèvora, donya Nadala esmenta que es tocarà la «Marxa de les torxes» del temps dels romans  ... 
doi:10.5944/rllcgv.vol.19.2014.13762 fatcat:jltqplxtsnezrlllj72zl2ql2e

«Josep és el nom més senyor que hi ha!»: onomàstica literària guimeraniana

Maridés Soler
2018 Revista de lenguas y literaturas catalana gallega y vasca  
En algunes cartes a Artur Vinardell(Guimerà 1978(Guimerà : 1485(Guimerà , 1487, confirma el seu desig que les traduccions de les seves obres siguin fidels i literals.  ...  ha volgut»; pel contrari, el Joan, que l'ha guanyada, comentarà: «Jesús, sí, mira-la» (MS: 969), i temeran Bujavà, Satanàs o Llucífer; els musulmans, per la seva banda, imploraran Al·là i Mahoma; els romans  ... 
doi:10.5944/rllcgv.vol.22.2017.20853 fatcat:ewf5lrli75dghjvjic4ldg5u3a

Page 99 of Hispania Vol. 3, Issue 2 [page]

1920 Hispania  
The following is a list of these playwrights, with the number of translations of their plays that have been published (it should be noted that two of these Spanish dramatists, Guimera and Rusifiol, write  ...  Bost. 1918. * Translations of the eleven following plays have been added to the list published in the Romanic Review: Alarcon (Mariano), Hijos de Adén; Ave- llaneda, Baltasar; Calder6n, El mdgico prodigioso  ... 

The castle of Loarre and his Romanesque door

Francesca Español Bertran
2006 Locus Amoenus  
El conde de Guimerá».  ...  Sobre la relación del conde de Guimerá con los materiales de su abuelo, resulta muy elocuente la nota inserta en el folio 3 (ms. 7534): «Don Gaspar de Castro y Pinós, Conde de Guimerá, Viz-conde de Evol  ... 
doi:10.5565/rev/locus.157 fatcat:5dlafaa4wnbthhgp5bgorv3xbe

Page 123 of Connoisseur, a Journal of Music and the Fine Arts Vol. 12, Issue 34 [page]

1898 Connoisseur, a Journal of Music and the Fine Arts  
Pas plus que dans ses romans, a mon sens, M. d’Annunzio n’y a révélé le don de faire vivre et parler des ames.  ...  Les Terres Basses d'un Espagnol encore, Angel Guimera, drame féroce de grande allure, offre —- mais porté au tra- gique et sur un ton beaucoup plus moderne le méme caractére national de simplification  ... 

Page 175 of Nuova Antologia, Revista Di Lettere, Scienze Ed Arti Vol. 197, Issue [page]

1904 Nuova Antologia, Revista Di Lettere, Scienze Ed Arti  
Angel Guimerà, i due poeti del Guatemala Pio M. Ri:ipele e Guillermo P.  ...  Roman von KARL PERFALL. — Berlin, Egon Fleischel u. C o. Allesamt Sùnder. Novellen von HENNY KosenBAUM. — Miinchen, Friedrich Rothbarth.  ... 
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