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Martin Smith
puts the fun in functional annotation
puts the fun in functional annotation
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Bioplatforms Australia and CSIRO would like to call for expressions of interest in hands-on bioinformatics workshops, in order to help us plan future workshops and events. Bioplatforms Australia, in partnership with CSIRO Bioinformatics Core, has…
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Our Cell paper is out! Check out the video abstract for the lazy. This method has the potential take our understanding of RNA-based regulation to a completely new level: transcriptome-wide maps of RNA-RNA interactions. It also shows that the XIST lncRNA forms large structured domains and that its RepA regions pair together, instead of forming distinct structures (which no one seemed to agree on).
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Some cool genomics from the Hayes lab, overly simplified for my taste but riveting nonetheless !
Catalyst
Catalyst
iview.abc.net.au
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My colleague Dessislava's entry for STEM:women in science
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Triple double Indian burritos!
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Feeding some wild-ish Rosellas in the Blue Mountains
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A 60 min summary of how most of our genome functions: through RNA!
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So running "grep -A 5 -m 1 pattern file" only returns one line, instead of the intuitive output of 5. WTF? #gnu  
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Get NGSANE from the BauerLab's github here: 
https://github.com/BauerLab/ngsane/wiki

Outline of NGSANE, a hot swappable modular framework for terabyte-scale data analysis. (A) A configuration file is created, or modified from a template, which specifies the details of an analysis. This includes the location of input files, the task (mod) to execute, runtime settings, and any custom parameters to implement. (B) The header.sh file contains general system variables, platform-specific parameters, and paths to the various software binaries installed on a system. This file needs to be configured once upon initial installation, then modified whenever new software versions are required. (C) The trigger.sh file is the main executable file in NGSANE. It processes the variables and tasks specified in the configuration files, ensuring that all dependencies are met and invoking the core job submission protocols. It allows the user to selectively launch a test or 'dry' run, a full high performance computing run, or generate a summary report once the tasks have completed. (D) The mod files contain the generic analytic pipelines that are to be executed on the HPC cluster. Each mod corresponds to a specific analysis, a single task, or a series thereof. They include checkpoints to recover previous failed executions, as well as comprehensive logging of each step. Advanced users can create customised mods and include them in the framework. (E) A concise and easy to read summary can be generated after completion of a task in HTML format. This usually includes general statistics of the results, including graphs, potential errors, and a itemised log of the checkpoints for each task.
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