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how_to [2019/07/03 19:24]
admin [Install R locally (e.g. on a cluster)?]
how_to [2019/07/08 20:56] (current)
admin [Install R locally (e.g. on a cluster)?]
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-**Begin learning bioinformatics?​** \\+====   Begin learning bioinformatics? ​  ==== 
 Take a course from the [[http://​research.omicsgroup.org/​index.php/​List_of_free_online_bioinformatics_courses|list]] of free online bioinformatics courses e.g., the Computational Molecular Biology [[http://​cmgm.stanford.edu/​biochem218/​index.html|Course]] at Stanford is broad and covers the classic topics but it is not updated, and may become outdated. The same is true for PLOS Translational Bioinformatics [[http://​collections.plos.org/​translational-bioinformatics|Collection]] of articles, which are more advanced. Most central topics are covered in some course from the European Bioinformatics Institute ([[https://​www.ebi.ac.uk/​training/​online/​course-list|EBI]]). Very useful training materials are available from [[https://​www.mygoblet.org/​|GOBLET]]. Videos from the Models, Inference & Algorithms Initiative ([[https://​www.broadinstitute.org/​scientific-community/​science/​mia/​models-inference-algorithms|MIA]]) at Broad are relatively advanced.\\ Take a course from the [[http://​research.omicsgroup.org/​index.php/​List_of_free_online_bioinformatics_courses|list]] of free online bioinformatics courses e.g., the Computational Molecular Biology [[http://​cmgm.stanford.edu/​biochem218/​index.html|Course]] at Stanford is broad and covers the classic topics but it is not updated, and may become outdated. The same is true for PLOS Translational Bioinformatics [[http://​collections.plos.org/​translational-bioinformatics|Collection]] of articles, which are more advanced. Most central topics are covered in some course from the European Bioinformatics Institute ([[https://​www.ebi.ac.uk/​training/​online/​course-list|EBI]]). Very useful training materials are available from [[https://​www.mygoblet.org/​|GOBLET]]. Videos from the Models, Inference & Algorithms Initiative ([[https://​www.broadinstitute.org/​scientific-community/​science/​mia/​models-inference-algorithms|MIA]]) at Broad are relatively advanced.\\
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-**Install Salmon on OSX?** \\+====   Install Salmon on OSX?   ==== 
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 If you do not have autoconf, [[http://​mac-dev-env.patrickbougie.com/​autoconf/​|install]] it. Following the installation guidelines, for OSX you need to first [[http://​stackoverflow.com/​questions/​3181468/​how-do-you-install-intel-tbb-on-os-x|install]] Thread Building Blocks (TBB) (brew install tbb) and then check that the installation was successful (brew list). Download the latest [[https://​github.com/​COMBINE-lab/​salmon/​releases|version]] of Salmon source code and uncompress it. Follow Salmon'​s installation [[http://​salmon.readthedocs.org/​en/​latest/​building.html#​installation|guidelines]]. The cmake command in the guidelines will be something like the following for OSX: If you do not have autoconf, [[http://​mac-dev-env.patrickbougie.com/​autoconf/​|install]] it. Following the installation guidelines, for OSX you need to first [[http://​stackoverflow.com/​questions/​3181468/​how-do-you-install-intel-tbb-on-os-x|install]] Thread Building Blocks (TBB) (brew install tbb) and then check that the installation was successful (brew list). Download the latest [[https://​github.com/​COMBINE-lab/​salmon/​releases|version]] of Salmon source code and uncompress it. Follow Salmon'​s installation [[http://​salmon.readthedocs.org/​en/​latest/​building.html#​installation|guidelines]]. The cmake command in the guidelines will be something like the following for OSX: