Grup de Recerca en Anàlisi Estadística de la Supervivència. GRASS

Exposició GRASS

Conferenciants: Moisés Gómez i Xavier de Pedro - Dimarts 5 de juny 2012

 

* 10:00 - Exposició Moisés: Proposta de tesi: Extensions, Applications and Computational Tools of the Asymptotic Relative Efficiency Method to choose the Primary Endpoint in a Clinical Trial (1h).

* 11:00 - Xavier de Pedro i Àlex Sànchez: Web interfaces for R scripts using Tiki and PluginR (2h).


Resum:
The need to work with colleagues from other institutions is very common around Academia and Science. Teams often find tools to communicate and coordinate with other web platforms to improve collaboration across space and time. Although analysis and visualization of data with R is becoming very popular, development teams frequently look also for web-based graphical user interfaces for the end users of those R scripts.


The list of prototypes and publicly announced free tools (R 2011) includes programs of all kinds. However, a quick review of these tools led us to similar conclusion reached by other researchers such as Saunders (2009): most of these programs seem to present problems in the short to medium term. Those problems arise from the fact that either such programs no longer work with current stable versions of standard and free web technology, because its development seems to have been discontinued for years. Or because they are too difficult to install or use for most scientists or people who are not professionals in web technology. 

Therefore, we decided in our research groups to contribute to the development of a relatively new approach, different from the latest approaches presented in the latest years (Ooms 2009, Nakano and Nakama 2009 and others): a plugin for Tiki Wiki CMS Groupware (also known as ”Tiki”), a mature collaborative web 2.0 framework released as free/libre open source software, somewhat similar to the R extension for Mediawiki, but with all the extra features from this “Tightly Integrated Knowledge Infrastructure“ that Tiki represents), along with its decentralized but truly successful development model (Tiki 2011).


This new PluginR (De Pedro 2011), has so far allowed the development of a Web application of use in research on the Teaching and Learning field (De Pedro et al. 2010), as well as to develop web interfaces for Basic Pipelines in Bioinformatics for medical research (De Pedro & Sánchez 2011a). 

The talk will highlight the main advantages (and disadvantages) found up to date with the use of Tiki + PluginR to solve many of the needs of our research groups, including the new progresses achieved after the presentation at the last Spanish R Users meeting (De Pedro & Sánchez 2010, 2011b).

 

Bibliografia:

  • De Pedro, X.; Sánchez, A. (2010). Usando de forma segura R vía web con Tiki. Presentació comunicació, II Jornadas (I Congreso) de Usuarios de R en castellano. Mieres, Oviedo, Spain. http://www.r-es.org/II+Jornadas - Full text |Slides
  • De Pedro, X.; Calvo, M.; Carnicer, A.; Cuadros, J.; Miñarro, A. (2010). Assessing student activity through log analysis from computer supported learning assignments. Presentació comunicació, 6º Congreso Internacional de Docencia Universitaria e Innovación - VI CIDUI. Barcelona, Spain.
  • De Pedro, X.; Sánchez, A. (2011a). Using R through a Tiki web interface to implement bioinformatics pipelines. Poster, 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology 2011 (ISMB/ECCB), N36. Vienna, ÀUSTRIA. http://posters.f1000.com/P1816
  • De Pedro, X.; Sánchez, A. (2011b). Novedades de Tiki y el PluginR en 2011: interfaces web más fáciles para programas en R. III Jornadas de Usuarios de R en castellano. Madrid, Spain. http://www.r-es.org/III+Jornadas -http://ueb.vhir.org/2011+R-es
  • De Pedro, X. (2011). Tiki documentation: Plugin R. https://doc.tiki.org/PluginR
  • Nakano, J. and E.-j. Nakama (2009). Web interface to r for high-performance computing. In The R UseR Conference 2009, Rennes.
  • Ooms, J. (2009). Building web applications with r. In The R UseR Conference 2009, Rennes.
  • R (2011). R faq. cran.r-project.org/doc/FAQ/R-FAQ.html#R-Web-Interfaces.
  • Saunders, N. (2009). A brief survey of r web interfaces. http://nsaunders.wordpress.com/2009/11/30/a-brief-survey-of-r-web-interfaces/
  • Tiki (2011). Development model. https://tiki.org/Model.