RNA World (beta)
RNA World (beta) is a volunteer distributed computing project that uses the BOINC platform and needs your help to advance RNA-related research.
Why RNA World (beta)?
Every protein in a cell is produced from a transiently synthesized messenger molecule, termed mRNA. This mRNA is then recognized by a cellular machinery that translates the base sequence of mRNA into its corresponding protein (which is a sequence of amino acids). This protein synthesis machinery, termed ribosome, is actually a ribozyme, i.e. it is a catalytically active assembly of several RNA molecules. Consequently, RNAs do not only serve as messenger molecules or perform structural functions as e.g. in tRNA but may also act as catalysts that perform biochemical reactions as is the case for protein enzymes. Of course, the ribosome also contains numerous proteins as it is a very complex ribonucleoprotein particle but these predominantly serve structural functions, e.g. to give the ribosome its shape.
Fascinatingly, the initial analysis of the human genome sequence revealed that, apparently, only a very small fraction of the DNA of our genome is encoding proteins. Scientists at first thought "what is all this junk DNA about?" or "can't we just delete it?". Today, it has become clear that probably a major fraction of regulatory events taking place in a human cell might be governed by small RNAs, the so-called miRNAs. Among other functions, these appear responsible for making sure that a skin cell becomes a skin cell while a muscle, liver or hair cell differentiates to a muscle, liver or hair cell during development and all this although the genetic material (DNA) of all of these very different cell types is essentially identical. On top of that it seems that many cancer types are accompanied by or even result from a deregulated miRNA profile in the affected cell. Moreover, viruses have been discovered to bring along miRNAs to modify the target cell's regulatory network leading to diseases.
Hence, it can be clearly stated that RNA research, e.g. by supporting the RNA World distributed supercomputer project, will ultimately lead to important discoveries that might also have significant impact on future health care.
Goal
RNA World is a volunteer distributed supercomputer that uses Internet-connected computers to advance RNA research. This system is dedicated to identify, analyze, structurally predict and design RNA molecules on the basis of established bioinformatics software in a high-performance, high-throughput fashion.
In contrast to classical bioinformatic approaches, RNA World does not rely on individual desktop computers, web servers or supercomputers. Instead, it represents a continuously evolving cluster of world-wide distributed machines of any type. As such, RNA World is very heterogenous and, depending on the sub-project, currently addresses Internet-connected computers running Linux, Windows and OSX operating systems - your computer could be an important part of it. The fact that hardware and electricity costs are shared among the volunteer contributors raises the possibility of performing interesting analyses which under economical aspects would often not be affordable. In return, RNA World is not for profit, exclusively uses open source code and will make its results available to the public.
In its present form, RNA World runs a fully automated high-throughput analysis software version of Infernal1, a program suite originally developed in Sean Eddys laboratory for the systematic identification of non-coding RNAs. The goal of this RNA World sub-project is to systematically identify all known RNA family members in all organisms known to date and make the results available to the public in a timely fashion. With your help, we also aim at supplying established bioinformatic databases such as Rfam2 with our results to help reduce their future maintenance costs.
In contrast to other distributed and grid computing projects, the RNA World developers are currently designing generalized user interfaces that, in parallel to the projects our own research team is following up, allow non-associated individual scientists to submit their own projects in a manner similar to using a web server interface - of course, free of cost.https://www.rechenkraft.net/wiki/RNA_World/Project_description/en
Also see scientific objectives here.
Methods
Important information for users with VirtualBox installed
If you have VirtualBox installed on your computer and participate in this project please note:
* in order to get tasks your CPU needs to have virtualisation capabilities (AMD-v or VT-x)
* those virtualisation capabilities need to be enabled in your BIOS settings or all tasks will error out
* Some tasks are incompatible with newer VirtualBox versions: If you have 1.15 or earlier tasks, you must use VirtualBox 4.3.x or earlier. If you have 1.17 tasks, you must use VirtualBox 5.0.x or earlier. If you have 1.18 tasks, you may use VirtualBox 5.1.x. If you have 1.19 tasks, you may use VirtualBox 5.2.x.
* a BOINC client of at least 7.2.33 is recommended
* The runtime of the cmsearch VM apps are very long (>1000 hours) and deadlines are automatically extended but only visible on the website!
Project team / Sponsors
This project was created within the Apothekerkraft.net eV association and is operated exclusively by volunteers. The cooperation partners are the Philipps University of Marburg and the Indian Institute of Science in Bangalore (India).
RNA World is run byrechner.net eV in Germany.
RNA World Personal (active development team)
class="wikitable"
project Manager
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Server administrator
Christian Beer & Uwe Beckert ( Yoyo )
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Software development
Christian Beer, Tilman Giese (coturnix), Volker Hatzenberger (Ananas), Nico Mittenzwey (Nico), Stephan Ude (Mueslirocker)
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Graphics & Design
Lasse J. Kolb, Rebirther, Dr. Michael HW Weber
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mw @ rnaworld.de
RNA World Staff (former members)
* Martin (Linuxfan) Bertheau: BOINC progress bar, Linux checkpointing
* Jacques Kühl: General checkpointing mechanism
* Maximilian (mxplm) Palm: Development of the "job submission" interface for end users
* Andre Schmitz (Grodahn): ARM software development
Scientific publications
# Hoch, Philipp G., Olga Y. Burenina, Michael H.W. Weber, Daria A. Elkina, Mikhail V. Nesterchuk, Petr V. Sergiev, Roland K. Hartmann and Elena A. Kubareva. Phenotypic characterization and complementation analysis of Bacillus subtilis 6S RNA single and double deletion mutants. Biochimie (2015). DOI: 10.1016/j.biochi.2014.12.019.
# Sinha, Akesh, Caroline Köhrer, Michael H.W. Weber, Isao Masuda, Vamsi K. Mootha, Ya-Ming Hou and Uttam L. RajBhandary. Biochemical Characterization of Pathogenic Mutations in Human Mitochondrial Methionyl-tRNA Formyltransferase. Journal of Biological Chemistry (2014). DOI: 10.1074/jbc.M114.610626.
# Arora, Smriti, Satya Prathyusha Bhamidimarri, Michael H. W. Weber and Umesh Varshney. Role of the Ribosomal P-Site Elements of m 2 G966, m 5 C967, and the S9 C-Terminal Tail in Maintenance of the Reading Frame during Translational Elongation in Escherichia coli. Journal of Bacteriology (2013). DOI: 10.1128/JB.00455-13.
# Arora, S., S. P. Bhamidimarri, M. Bhattacharyya, A. Govindan, M. H. W. Weber, S. Vishveshwara and U. Varshney. Distinctive contributions of the ribosomal P-site elements m2G966, m5C967 and the C-terminal tail of the S9 protein in the fidelity of initiation of translation in Escherichia coli. Nucleic Acids Research (2013). DOI: 10.1093/nar/gkt175.
# Seshadri, Anuradha, Badrinath Dubey, Michael H. W. Weber and Umesh Varshney. Impact of rRNA methylations on ribosome recycling and fidelity of initiation in Escherichia coli. Molecular Microbiology (2009). DOI: 10.1111/j.1365-2958.2009.06685.x.
