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Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example

Yoshinobu Kano, Ngan Nguyen, Rune Saetre, Kazuhiro Yoshida, Yusuke Miyao, Yoshimasa Tsuruoka, Yuichiro Matsubayashi, Sophia Ananiadou, Jun'ichi Tsujii
2008 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
In this paper, we describe such an environment that was developed based on UIMA, and we show its feasibility through our experience in developing a protein-protein interaction (PPI) extraction system.  ...  comparisons of available tools, a simple I/O interface, and visualization tools.  ...  Lawrence Hunter's text mining group at the Center for Computational Pharmacology for discussing with us and making their tools available for this research.  ... 
pmid:18229720 fatcat:wrzulyl2drbfthmivumqttd32y

Gexplora – user interface that highlights and explores the density of genomic elements along a chromosomal sequence [article]

Thomas Nussbaumer, Olivia Debnath, Parviz Heidari
2020 bioRxiv   pre-print
, OMA and STRING database using REST API calls to retrieve sequence-intrinsic information, protein-protein datasets and orthologous groups.  ...  AbstractThe density of genomic elements such as genes or transposable elements along its consecutive sequence can provide an overview of a genomic sequence while in the detailed analysis of candidate genes  ...  Other technical aspects include the improvements of computational tools for read assembly 11 and strategies to filter reads prior to analysis 13 as well as approaches to perform gap-filling 14 .  ... 
doi:10.1101/2020.04.04.025379 fatcat:mxcct3z3jjc6dpl3ppo5gia2tm

P2P Mapper: From User Experiences to Pattern-Based Design

Homa Javahery, Ahmed Seffah
2012 AIS Transactions on Human-Computer Interaction  
User experience is an umbrella term referring to a collection of information that covers the user's behavior and interaction with a system.  ...  It is observed when the user is actively using a service or interacting with information, includes expectations and perceptions, and is influenced by user characteristics and application or service characteristics  ...  THE SECOND STUDY: DESIGNING WITH THE P2P MAPPER We used the P2P Mapper tool to redesign a tool called Protein Explorer used to visualize biological data.  ... 
doi:10.17705/1thci.00042 fatcat:ab7ltbeegfffrhum727houyyna

Supporting cognition in systems biology analysis: findings on users' processes and design implications

Barbara Mirel
2009 Journal of Biomedical Discovery and Collaboration  
Researchers interacted with the same proteinprotein interaction tools to discover possible disease mechanisms for further experimentation.  ...  for formulating plausible and credible hypotheses.  ...  I thank Zach Wright for contributions to collecting and analyzing data and am grateful to the anonymous reviewers for their helpful comments and suggestions.  ... 
doi:10.1186/1747-5333-4-2 pmid:19216777 pmcid:PMC2649900 fatcat:zgi75ipuorgstltuxbiph4nshm

Molecular Architect: A User-Friendly Workflow for Virtual Screening

Eduardo H. B. Maia, Lucas Rolim Medaglia, Alisson Marques da Silva, Alex G. Taranto
2020 ACS Omega  
Many free tools are available for this purpose, but they are difficult to use and do not have a graphical user interface.  ...  MolAr is a workflow with a simple and intuitive interface that acts in an integrated and automated form to perform the entire VS process, from protein preparation (homology modeling and protonation state  ...  Author Contributions All authors contributed to writing the manuscript, and all authors approved the final version of the manuscript.  ... 
doi:10.1021/acsomega.9b04403 pmid:32258898 pmcid:PMC7114615 fatcat:2tmcblaehvfs7fjr3347e4cu2y

BrainWiki—A Wiki-Style, User Driven, Comparative Brain Anatomy Tool

Linda Forsell, Esther Naomi Vos, Keerthi Jayaraman, Axel Edman, S. Abid Hussaini
2020 Frontiers in Neuroanatomy  
The website relies on interactivity and supports user contributions resulting in a dynamic website that evolves at the pace of neuroscience.  ...  We present BrainWiki, a user-friendly, web-based atlas that links the human and the mouse brain together, side-by-side.  ...  We would like to thank Allen Institute for Brain Science for making the images and the API available for us to use freely. We thank Sidney Rehn for providing the voice over for the How To videos.  ... 
doi:10.3389/fnana.2020.548172 pmid:33192339 pmcid:PMC7604473 fatcat:6ibdeamig5gatj4qc4iksadxpi

POSA: a user-driven, interactive multiple protein structure alignment server

Zhanwen Li, Padmaja Natarajan, Yuzhen Ye, Thomas Hrabe, Adam Godzik
2014 Nucleic Acids Research  
The second improvement is an interactive visualization with options that allow the user to view all superposed structures in one window (a typical solution for visualizing results of multiple structure  ...  The user can rotate structure(s) in any of the windows and study similarities or differences between structures clearly visible in individual windows.  ...  ACKNOWLEDGMENT We thank Drs Alexey Eroshkin and Lukasz Jaroszewski of Sanford-Burnham Medical Research Institute, La Jolla, CA, for their suggestions for the POSA upgrade.  ... 
doi:10.1093/nar/gku394 pmid:24838569 pmcid:PMC4086100 fatcat:quojw6yewncvzksa5t6rkyre6m

BioAssemblyModeler (BAM): User-Friendly Homology Modeling of Protein Homo- and Heterooligomers

Maxim V. Shapovalov, Qiang Wang, Qifang Xu, Mark Andrake, Roland L. Dunbrack, Lukasz Kurgan
2014 PLoS ONE  
BAM takes as input up to six different protein sequences and begins by assigning Pfam domains to the target sequences.  ...  BioAssemblyModeler (BAM) is a graphical user interface to the basic steps in homology modeling of protein homooligomers and heterooligomers from the biological assemblies provided in the PDB.  ...  Results and Discussion An example session of modeling a heterohexameric complex is shown in Figure 1 .  ... 
doi:10.1371/journal.pone.0098309 pmid:24922057 pmcid:PMC4055448 fatcat:yqltwfr7jfdy7jnqskbqqmtmmy

WHAM!: a web-based visualization suite for user-defined analysis of metagenomic shotgun sequencing data

Joseph C. Devlin, Thomas Battaglia, Martin J. Blaser, Kelly V. Ruggles
2018 BMC Genomics  
as a web-based interactive tool capable of user-directed data visualization and statistical analysis of annotated shotgun metagenomic and metatranscriptomic data sets. WHAM!  ...  is an interactive and customizable tool for downstream metagenomic and metatranscriptomic analysis providing a user-friendly interface allowing for easy data exploration by microbiome and ecological experts  ...  Acknowledgements This work has used computing resources at the NYU High Performance Computing Facility (HPCF).  ... 
doi:10.1186/s12864-018-4870-z pmid:29940835 pmcid:PMC6019711 fatcat:oyp5kvk4lfgzxevkwipahi4o3q

Towards user-centric concrete model transformation

I. Avazpour
2012 2012 IEEE Symposium on Visual Languages and Human-Centric Computing (VL/HCC)  
To generate a transformation with most current MDE approaches, users are required to specify (or provide) complex abstractions and meta-models and engage in quite lowlevel coding in usually textual transformation  ...  Model transformations are an important part of Model Driven Engineering (MDE).  ...  A PPI network is a graph in which each node corresponds to a protein and an edge indicates a direct physical interaction between proteins.  ... 
doi:10.1109/vlhcc.2012.6344520 dblp:conf/vl/Avazpour12 fatcat:izqupk5eubhalhgrfahy7y3cbm

Usability and user experience evaluation of natural user interfaces: a systematic mapping study

Guilherme Corredato Guerino, Natasha Malveira Costa Valentim
2020 IET Software  
For future work, they intend to develop an evaluation technology for NUIs that fills the gaps identified in their SMS and combining Usability and UX.  ...  In the software development process, usability and user eXperience (UX) evaluations are a relevant step, since they evaluate several aspects of the system, such as efficiency, effectiveness, user satisfaction  ...  Therefore, our SMS aimed to fill this gap, checking the state-of-the-art of technologies used to evaluate usability and UX in the general context of NUIs.  ... 
doi:10.1049/iet-sen.2020.0051 fatcat:5v5ojomnmvhx5fbc2jgrche3qm

User-friendly 3D bioassays with cell-containing hydrogel modules: narrowing the gap between microfluidic bioassays and clinical end-users' needs

Do-Hyun Lee, Chae Yun Bae, Seyong Kwon, Je-Kyun Park
2015 Lab on a Chip  
This frontier article reviews recent progress in the development and application of user-friendly 3D bioassay techniques combined with cell-containing hydrogel modules.  ...  Notes and references  ...  in an open type of microchannel that uses surface tension to fill and maintain a fluid in microscale structures devoid of a ceiling and floor, known as suspended microfluidics. 38 This approach was used  ... 
doi:10.1039/c5lc00239g pmid:25857752 fatcat:n6ydc37pkzcg7m34yaxccqxkca


Aran Lunzer, Kasper Hornbæk
2006 Proceedings of the 19th annual ACM symposium on User interface software and technology - UIST '06  
We present the Re-cipeSheet, a general-purpose tool for assisting users in such tasks.  ...  The RecipeSheet lets users create information processors, called recipes, which may take input in a variety of forms such as text, Web pages, or XML, and produce results in a similar variety of forms.  ...  of XQuery; and the many bioinformatics tools, and other Web applications and Web services, that we have used as examples.  ... 
doi:10.1145/1166253.1166276 dblp:conf/uist/LunzerH06 fatcat:zsssdcu3ojeilanwtsfp5cp6ru

Multiple sequence alignment with user-defined anchor points

Burkhard Morgenstern, Sonja J Prohaska, Dirk Pöhler, Peter F Stadler
2006 Algorithms for Molecular Biology  
As a demonstration of how our method works, we apply our approach to genomic sequences around the Hox gene cluster and to a set of DNA-binding proteins.  ...  As a by-product, we obtain insights about the performance of the greedy algorithm that our program uses for multiple alignment and about the underlying objective function.  ...  Acknowledgements We would like to thank Jan Weyer-Menkhoff, Isabelle Schneider, Rasmus Steinkamp and Amarendran Subramanian for their support in the software development and evaluation and Peter Meinicke  ... 
doi:10.1186/1748-7188-1-6 pmid:16722533 pmcid:PMC1481597 fatcat:gylmuahr7zb4jainalgug47tne

Knowledge discovery in high-dimensional data: case studies and a user survey for the rank-by-feature framework

Jinwook Seo, B. Shneiderman
2006 IEEE Transactions on Visualization and Computer Graphics  
This paper presents an evaluation of the Hierarchical Clustering Explorer (HCE) using three case studies and an email user survey (n=57) to focus on skill acquisition with the novel concepts and interface  ...  Our 3-year effort to develop versions of the Hierarchical Clustering Explorer (HCE) began with building an interactive tool for exploring clustering results.  ...  Acknowledgement: This work was supported by N01 NS-1-2339 from the NIH and by the National Science Foundation under Grant No. EIA 0129978.  ... 
doi:10.1109/tvcg.2006.50 pmid:16640245 fatcat:chg2hdfvfvfijjpzsbwcsyayre
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