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F1000Research, Volume 3
Volume 3, 2014
- Carly Strasser, John A. Kunze
, Stephen Abrams
DataUp: A tool to help researchers describe and share tabular data. 6 - Soma Ghosh
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
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
PPI layouts: BioJS components for the display of Protein-Protein Interactions. 50 - Alex Kalderimis, Radek Stepan, Julie M. Sullivan
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
wigExplorer, a BioJS component to visualise wig data. 53 - Manuel Corpas
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
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
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
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
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
GASOLINE: a Cytoscape app for multiple local alignment of PPI networks. 140 - Ruth Isserlin
Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results. 141 - Keiichiro Ono
Cytoscape tools for the web age: D3.js and Cytoscape.js exporters. 143 - Kozo Nishida
KEGGscape: a Cytoscape app for pathway data integration. 144 - Guanming Wu
ReactomeFIViz: the Reactome FI Cytoscape app for pathway and network-based data analysis. 146 - John H. Morris
enhancedGraphics: a Cytoscape app for enhanced node graphics. 147 - Jianjiong Gao
BridgeDb app: unifying identifier mapping services for Cytoscape. 148 - John H. Morris
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
Cytoscape: the network visualization tool for GenomeSpace workflows. 151 - Hui Hsien Wu, Edward D. Lemaire
Combining low sampling frequency smartphone sensors and video for a Wearable Mobility Monitoring System. 170 - Kristina M. Hettne
Explain your data by Concept Profile Analysis Web Services. 173 - Patrizio Tressoldi
Brain-to-Brain (mind-to-mind) interaction at distance: a confirmatory study. 182 - Stephen J. Beckett
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
Detecting miRNA Mentions and Relations in Biomedical Literature. 205 - Sandeep Chakraborty
PAGAL - Properties and corresponding graphics of alpha helical structures in proteins. 206 - Sreeram V. Ramagopalan
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
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
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
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
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
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
PRN: a preprint service for catalyzing R-fMRI and neuroscience related studies. 313
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