Phage spanins: diversity, topological dynamics and gene convergence

Autor: Rohit Kongari, Manoj Rajaure, Jesse Cahill, Eric Rasche, Eleni Mijalis, Joel Berry, Ry Young

Publikováno v: BMC Bioinformatics, Vol 19, Iss 1, Pp 1-26 (2018)

Abstract Background Spanins are phage lysis proteins required to disrupt the outer membrane. Phages employ either two-component spanins or unimolecular spanins in this final step of Gram-negative host lysis. Two-component spanins like Rz-Rz1 from pha

Externí odkaz: https://doaj.org/article/c60df76c6b9643368035cea84344fdbe

Jupyter and Galaxy: Easing entry barriers into complex data analyses for biomedical researchers.

Autor: Björn A Grüning, Eric Rasche, Boris Rebolledo-Jaramillo, Carl Eberhard, Torsten Houwaart, John Chilton, Nate Coraor, Rolf Backofen, James Taylor, Anton Nekrutenko

Publikováno v: PLoS Computational Biology, Vol 13, Iss 5, p e1005425 (2017)

What does it take to convert a heap of sequencing data into a publishable result? First, common tools are employed to reduce primary data (sequencing reads) to a form suitable for further analyses (i.e., the list of variable sites). The subsequent ex

Externí odkaz: https://doaj.org/article/b9ffb2544292468abd071231c8278d0e

Bioconda: A sustainable and comprehensive software distribution for the life sciences

Autor: Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Adam Caprez, Bérénice Batut, Mathias Haudgaard, Thomas Cokelaer, Kyle A. Beauchamp, Brent S Pedersen, Youri Hoogstrate, Anthony Bretaudeau, Devon Ryan, Gildas Le Corguillé, Dilmurat Yusuf, Sebastian Luna-Valero, Rory Kirchner, Karel Brinda, Thomas Wollmann, Martin Raden, Simon J. van Heeringen, Nicola Soranzo, Lorena Pantano, Zachary Charlop-Powers, Per Unneberg, Matthias De Smet, Marcel Martin, Greg Von Kuster, Tiago Antao, Milad Miladi, Kevin Thornton, Christian Brueffer, Marius van den Beek, Daniel Maticzka, Clemens Blank, Sebastian Will, K´evin Gravouil, Joachim Wolff, Manuel Holtgrewe, Jörg Fallmann, Vitor C. Piro, Ilya Shlyakhter, Ayman Yousif, Philip Mabon, Xiao-Ou Zhang, Wei Shen, Jennifer Cabral, Cristel Thomas, Eric Enns, Joseph Brown, Jorrit Boekel, Mattias de Hollander, Jerome Kelleher, Nitesh Turaga, Julian R. de Ruiter, Dave Bouvier, Simon Gladman, Saket Choudhary, Nicholas Harding, Florian Eggenhofer, Arne Kratz, Zhuoqing Fang, Robert Kleinkauf, Henning Timm, Peter J. A. Cock, Enrico Seiler, Colin Brislawn, Hai Nguyen, Endre Bakken Stovner, Philip Ewels, Matt Chambers, James E. Johnson, Emil Hägglund, Simon Ye, Roman Valls Guimera, Elmar Pruesse, W. Augustine Dunn, Lance Parsons, Rob Patro, David Koppstein, Elena Grassi, Inken Wohlers, Alex Reynolds, MacIntosh Cornwell, Nicholas Stoler, Daniel Blankenberg, Guowei He, Marcel Bargull, Alexander Junge, Rick Farouni, Mallory Freeberg, Sourav Singh, Daniel R. Bogema, Fabio Cumbo, Liang-Bo Wang, David E Larson, Matthew L. Workentine, Upendra Kumar Devisetty, Sacha Laurent, Pierrick Roger, Xavier Garnier, Rasmus Agren, Aziz Khan, John M Eppley, Wei Li, Bianca Katharina Stöcker, Tobias Rausch, James Taylor, Patrick R. Wright, Adam P. Taranto, Davide Chicco, Bengt Sennblad, Jasmijn A. Baaijens, Matthew Gopez, Nezar Abdennur, Iain Milne, Jens Preussner, Luca Pinello, Avi Srivastava, Aroon T. Chande, Philip Reiner Kensche, Yuri Pirola, Michael Knudsen, Ino de Bruijn, Kai Blin, Giorgio Gonnella, Oana M. Enache, Vivek Rai, Nicholas R. Waters, Saskia Hiltemann, Matthew L. Bendall, Christoph Stahl, Alistair Miles, Yannick Boursin, Yasset Perez-Riverol, Sebastian Schmeier, Erik Clarke, Kevin Arvai, Matthieu Jung, Tom´as Di Domenico, Julien Seiler, Eric Rasche, Etienne Kornobis, Daniela Beisser, Sven Rahmann, Alexander S Mikheyev, Camy Tran, Jordi Capellades, Christopher Schröder, Adrian Emanuel Salatino, Simon Dirmeier, Timothy H. Webster, Oleksandr Moskalenko, Gordon Stephen, Johannes Köster

We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multiplatform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8624a7351a9f3f1f0c0e57beb5ff9386
https://doi.org/10.1101/207092

Enhancing pre-defined workflows with ad hoc analytics using Galaxy, Docker and Jupyter

Autor: Torsten Houwaart, Carl Eberhard, Nathan Coraor, John Chilton, Rolf Backofen, Anton Nekrutenko, Björn Grüning, James Taylor, Boris Rebolledo Jaramillo, Eric Rasche

What does it take to convert a heap of sequencing data into a publishable result? First, common tools are employed to reduce primary data (sequencing reads) to a form suitable for further analyses (i.e., list of variable sites). The subsequent explor

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d020c443a865148750975b8e17cbc57f

Complete Genome Sequence of Citrobacter freundii Myophage Merlin

Autor: Christopher L. Bernal, Jesse Cahill, Eric Rasche, Gabriel F. Kuty Everett, Victoria E. Berkowitz

Publikováno v: Genome Announcements

Bacteriophage Merlin is a T4-like myophage which infects Citrobacter freundii , a member of the Enterobacteriaceae family. C. freundii is an opportunistic pathogen that is a common cause of nosocomial infections. This report announces the complete ge

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::11534884749511fd045c65249ac439e4
https://doi.org/10.1128/genomea.01133-15