This is the PDF of the GenABEL tutorial, a book on how to use the GenABEL package and several other tools from the GenABEL suite (see. for the GenABEL project contributors. [ @GenAproj | www. . posts on forum. Open-source tutorial. GenABEL package. GenABEL suite. PredictA. PredictA. GenABEL tutorial. GenABEL tutorial Street, Suite , Mountain View, California, , USA. >= library(GenABEL) data( srdta) @.
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I therefore think this is overall a nice publication that is certainly suitable for indexation.
Archived source code at the time of publication https: Interaction with the user community is done via social media like Twitter https: To this end all program code and documentation are either stored in a publicly readable instance of the Subversion version control system, with write access limited to a group of core contributors, or on GitHub https: The code contained in tuyorial Org mode file and the data in the csv files listed above are in the public domain Creative Commons CC0 license and can be used without restriction.
The methodologies underlining the different tools and their potential applications are well described. Therefore, these were counted manually.
tutoriial I have read this submission. Consequently, changes that break existing functionality are detected at an early stage, thus leading to more stable software releases. It is my understanding that the manuscript is aimed at reaching potential new users, but even to old users, unaware of the possible new tools included in the GenABEL project. Moreover, compared to having individual users e-mailing a package author, who may be on holiday or otherwise unavailable, an open forum where users and developers collaborate helps in shortening the time-to-answer.
Nevertheless, despite limited amount of novel scientific ideas or scientific results in the current manuscript, the authors have clearly put a lot of work into creating a very impressive interactive user and developer community.
It contains a high-performance computing based approach facilitating extremely fast mixed-model based regression of multiple omics traits like metabolomics or lipidomics on imputed genotype data Ten simple rules for a successful cross-disciplinary collaboration.
Table 1 and two that are yenabel beta stage. Having an open forum serves various purposes. Conclusion The original publication of the GenABEL package for statistical analysis of genotype data 10 has led to the evolution of a community which we now genabdl the GenABEL project, which brings together geabel, software developers and tuorial users with the central goal ttuorial making statistical genomics work by openly developing and subsequently implementing statistical models into user-friendly software.
It is clear, from the texts, the effort that has taken place and is taking place aiming at bringing together top scientists, software developers and end users with the central goal of making statistical genomics work by openly developing tutkrial subsequently implementing statistical models into a user-friendly software.
The project has benefited from an open development model, facilitating communication and gsnabel sharing between the parties involved. OmicABEL aims to increase computational throughput while reducing memory usage and energy consumption. Indeed, this is reflected by more than citations according to google scholar for the original GenABEL paper published in Collins FS, Varmus H: This very well written article describes the GenABEL project for statistical genomics and high lightens the great success of the project, that in the years has lead to the creation of an actual scientific community that is spread in several countries worldwide.
A multi-language computing environment for literate programming and reproducible research.
The GenABEL Tutorial
The source code for the other packages can be downloaded from our website at http: Each tool in the GenABEL suite has its own documentation and the GenABEL Tutorial 27 with more than pages takes the user from learning basic R to performing more complicated analyses, showing how the various packages interconnect.
Published online May In short, it is a form of agile community-driven development 11 It is a computationally efficient solution for screening general forms of CH alleles in densely imputed microarray or whole genome sequencing datasets Ten simple rules for the open development of scientific software.
Moreover, public access to the source code is an important ingredient for active participation by people from outside the core development team and is paramount for reproducible research. J Am Med Inform Assoc.
With the help of computer scientists and scientific software developers these mathematical models are then implemented into efficient and user-friendly software. Increasing the power of genome wide association studies in natural populations using repeated measures-evaluation and implementation.
This was achieved by using optimal hardware-tailored algorithms using state-of-the-art linear algebra kernels, incorporating optimizations and avoiding redundant computations. Currently, a total of 94 bugs have been submitted to the bug trackers on R-forge and GitHub since their opening in andrespectively. Not only do we require that all tools are released under an open source or free software licence like the GNU Public Licence GPLwe also try to create an atmosphere of open communication using public mailing lists and web forums see the sections Interaction with the user community and Development infrastructure below.
Approved Giulietta MinozziReferee 1. Lastly, to reiterate, the GenABEL is a very impressive large scale project that is heavily used by the community! Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. Feedback from end users is actively encouraged through a web forum, which steadily grows into a knowledge base with a multitude of answered questions.
The authors declare no conflicts of interest in the authorship or publication of this contribution.
Support Center Support Center. Therefore, the community has the option to mark a tool as obsolete, warning the user that bugs will no longer be fixed and support is limited or non-existent.
Journal List FRes v.
All authors contributed to the review of the manuscript and agreed to the final content. First of all it is a central, easy to point to reference.