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F1000Research, Volume 3
Volume 3, 2014
- Carly Strasser, John A. Kunze
, Stephen Abrams
, Patricia Cruse:
DataUp: A tool to help researchers describe and share tabular data. 6 - Soma Ghosh
, Saraswathi Vishveshwara:
Ranking the quality of protein structure models using sidechain based network properties. 17 - Antonio Jimeno-Yepes, Karin Verspoor
:
Mutation extraction tools can be combined for robust recognition of genetic variants in the literature. 18 - Christopher R. Madan
, Marcia Spetch:
Visualizing and quantifying movement from pre-recorded videos: The spectral time-lapse (STL) algorithm. 19 - Caitlin M. Rivers, Bryan L. Lewis:
Ethical research standards in a world of big data. 38 - Alex Kalderimis, Radek Stepan, Julie M. Sullivan, Rachel Lyne, Michael Lyne, Gos Micklem
:
BioJS InterMine List Analysis: A BioJS component for displaying graphical or statistical analysis of collections of items from InterMine endpoints. 45 - Alex Kalderimis, Radek Stepan, Julie M. Sullivan, Rachel Lyne, Michael Lyne, Gos Micklem
:
BioJS InterMineTable Component: A BioJS component for displaying data from InterMine compatible webservice endpoints. 46 - Guy Yachdav, Maximilian Hecht, Metsada Pasmanik-Chor, Adva Yeheskel, Burkhard Rost
:
HeatMapViewer: interactive display of 2D data in biology. 48 - Gustavo A. Salazar
, Ayton Meintjes, Nicola J. Mulder
:
PPI layouts: BioJS components for the display of Protein-Protein Interactions. 50 - Alex Kalderimis, Radek Stepan, Julie M. Sullivan
, Rachel Lyne, Michael Lyne, Gos Micklem
:
BioJS DAGViewer: A reusable JavaScript component for displaying directed graphs. 51 - John Gómez, Rafael C. Jiménez
:
Sequence, a BioJS component for visualising sequences. 52 - Anil S. Thanki, Rafael C. Jiménez, Gemy G. Kaithakottil, Manuel Corpas
, Robert P. Davey
:
wigExplorer, a BioJS component to visualise wig data. 53 - Manuel Corpas
, Rafael C. Jiménez
, Seth Carbon, Alexander García Castro, Leyla Jael Castro
, Tatyana Goldberg, John Gómez, Alex Kalderimis, Suzanna E. Lewis, Ian Mulvany
, Aleksandra Pawlik, Francis Rowland
, Gustavo A. Salazar
, Fabian Schreiber, Ian Sillitoe, William Spooner, Anil S. Thanki
, Jose M. Villaveces, Guy Yachdav, Henning Hermjakob
:
BioJS: an open source standard for biological visualisation - its status in 2014. 55 - Manuel Corpas
:
The BioJS article collection of open source components for biological data visualisation. 56 - Greg Wilson:
Software Carpentry: lessons learned. 62 - Ye Hu, Jürgen Bajorath
:
Compound data sets and software tools for chemoinformatics and medicinal chemistry applications: update and data transfer. 69 - Zeeshan Ahmed
, Saman Zeeshan
, Thomas Dandekar:
Developing sustainable software solutions for bioinformatics by the "Butterfly" paradigm. 71 - Amalio Telenti, Erman Ayday, Jean-Pierre Hubaux:
On genomics, kin, and privacy. 80 - John Kratz, Carly Strasser:
Data publication consensus and controversies. 94 - Mariana Neves
:
An analysis on the entity annotations in biological corpora. 96 - Kenji Mizuseki
, Kamran Diba
, Eva Pastalkova, Jeffrey L. Teeters, Anton M. Sirota, György Buzsáki
:
Neurosharing: large-scale data sets (spike, LFP) recorded from the hippocampal-entorhinal system in behaving rats. 98 - Konrad Hinsen
:
Computational science: shifting the focus from tools to models. 101 - Claas-Thido Pfaff, Karin Nadrowski, Sophia Ratcliffe
, Christian Wirth, Helge Bruelheide:
Readable workflows need simple data. 110 - Tejas Desai, Manish Patwardhan, Hunter Coore
:
Factors that contribute to social media influence within an Internal Medicine Twitter learning community. 120 - Paige Brown, Rosanne M. Scholl:
Expert interviews with science communicators: How perceptions of audience values influence science communication values and practices. 128 - Alexander R. Pico
, Gary D. Bader
, Barry Demchak
, Oriol Guitart Pla, Timothy Hull, William J. R. Longabaugh, Christian Tannus Lopes, Samad Lotia, Piet Molenaar, Jason Montojo, John H. Morris
, Keiichiro Ono, Benno Schwikowski
, David Welker, Trey Ideker
:
The Cytoscape app article collection. 138 - Giovanni Scardoni, Gabriele Tosadori, Mohammed Faizan, Fausto Spoto, Franco Fabbri, Carlo Laudanna:
Biological network analysis with CentiScaPe: centralities and experimental dataset integration. 139 - Giovanni Micale
, Andrea Continella, Alfredo Ferro, Rosalba Giugno
, Alfredo Pulvirenti:
GASOLINE: a Cytoscape app for multiple local alignment of PPI networks. 140 - Ruth Isserlin
, Daniele Merico
, Veronique Voisin
, Gary D. Bader
:
Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results. 141 - Keiichiro Ono
, Barry Demchak
, Trey Ideker:
Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. 143 - Kozo Nishida
, Keiichiro Ono, Shigehiko Kanaya, Koichi Takahashi:
KEGGscape: a Cytoscape app for pathway data integration. 144 - Guanming Wu
, Eric T. Dawson
, Adrian Duong, Robin Haw
, Lincoln Stein:
ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis. 146 - John H. Morris
, Allan Kuchinsky, Thomas E. Ferrin
, Alexander R. Pico
:
enhancedGraphics: a Cytoscape app for enhanced node graphics. 147 - Jianjiong Gao
, Chao Zhang
, Martijn P. van Iersel
, Li Zhang, Dong Xu, Nikolaus Schultz
, Alexander R. Pico
:
BridgeDb app: unifying identifier mapping services for Cytoscape. 148 - John H. Morris
, Allan Wu, Nadezhda T. Doncheva
, Mario Albrecht, Thomas E. Ferrin
:
setsApp: Set operations for Cytoscape Nodes and Edges. 149 - David Welker, Barry Demchak
:
Porting and using PanGIA for Cytoscape 3: challenges and solutions. 150 - Barry Demchak
, Tim Hull, Michael Reich
, Ted Liefeld, Michael E. Smoot
, Trey Ideker, Jill P. Mesirov:
Cytoscape: the network visualization tool for GenomeSpace workflows. 151 - Hui Hsien Wu, Edward D. Lemaire
, Natalie Baddour
:
Combining low sampling frequency smartphone sensors and video for a Wearable Mobility Monitoring System. 170 - Kristina M. Hettne
, Reinout van Schouwen, Eleni Mina, Eelke van der Horst
, Mark Thompson, Rajaram Kaliyaperumal, Barend Mons, Erik M. van Mulligen
, Jan A. Kors, Marco Roos
:
Explain your data by Concept Profile Analysis Web Services. 173 - Patrizio Tressoldi
, Luciano Pederzoli
, Marco Bilucaglia
, Patrizio Caini, Pasquale Fedele
, Alessandro Ferrini, Simone Melloni, Diana Richeldi, Florentina Richeldi, Agostino Accardo:
Brain-to-Brain (mind-to-mind) interaction at distance: a confirmatory study. 182 - Stephen J. Beckett
, Chris A. Boulton
, Hywel T. P. Williams
:
FALCON: a software package for analysis of nestedness in bipartite networks. 185 - Charles W. Bangley, D. S. Shiffman:
Biology and conservation of elasmobranchs: an introduction to the collection. 192 - David M. Aanensen, Derek Huntley, Mirko Menegazzo, Chris I. Powell, Brian G. Spratt:
EpiCollect+: linking smartphones to web applications for complex data collection projects. 199 - Shweta Bagewadi Kawalia, Tamara Bobic, Martin Hofmann-Apitius
, Juliane Fluck, Roman Klinger:
Detecting miRNA Mentions and Relations in Biomedical Literature. 205 - Sandeep Chakraborty
, Basuthkar J. Rao, Abhay Dandekar
:
PAGAL - Properties and corresponding graphics of alpha helical structures in proteins. 206 - Sreeram V. Ramagopalan
, Radek Wasiak, Andrew P. Cox:
Using Twitter to investigate opinions about multiple sclerosis treatments: a descriptive, exploratory study. 216 - Vladimir Skornyakov, Maria Skornyakova, Antonina Shurygina, Pavel Skornyakov:
Finite-state discrete-time Markov chain models of gene regulatory networks. 220 - Christopher L. Dembia
, Jason Keith Moore
, Mont Hubbard:
An object oriented implementation of the Yeadon human inertia model. 223 - Michael Scott Brown, Tommy Bennett, James A. Coker
:
Niche Genetic Algorithms are better than traditional Genetic Algorithms for de novo Protein Folding. 236 - Matthew A. Helsby, Mei Yee Leung, Andrew D. Chalmers:
The F1000Research Antibody Validation Article Collection. 241 - Derek W. Wright
, Tim Angus, Anton J. Enright
, Tom C. Freeman:
Visualisation of BioPAX Networks using BioLayout Express3D. 246 - Andrew C. R. Martin
:
Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV). 249 - Nadia K. Litterman, Michele Rhee, David C. Swinney, Sean Ekins
:
Collaboration for rare disease drug discovery research. 261 - Peter D. Reiss
, Danxi Min, Mei Y. Leung:
Working towards a consensus for antibody validation. 266 - Bryan Ericksen
:
Safety, efficacy and utility of methods of transferring adhesive and cohesive Escherichia coli cells to microplates to avoid aerosols. 267 - Gonzalo Ruiz-Manrique
, Kazuhiro Tajima-Pozo, Francisco M. Ortuño Guzman:
Case Report: "ADHD Trainer": the mobile application that enhances cognitive skills in ADHD patients. 283 - Kazuki Oshita, Masaru Tomita, Kazuharu Arakawa:
G-Links: a gene-centric link acquisition service. 285 - Konrad Hinsen:
Platforms for publishing and archiving computer-aided research. 289 - Sandeep Chakraborty, My Phu, Basuthkar J. Rao, Bjarni Asgeirsson
, Abhay Dandekar
:
The PDB database is a rich source of alpha-helical anti-microbial peptides to combat disease causing pathogens. 295 - Craig McClain, Liz Neeley
:
A critical evaluation of science outreach via social media: its role and impact on scientists. 300 - David A. W. Soergel
:
Rampant software errors undermine scientific results. 303 - Chaogan Yan
, Qingyang Li, Lei Gao:
PRN: a preprint service for catalyzing R-fMRI and neuroscience related studies. 313
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