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| **Get familiar with machine learning and its applications in computational biology? ** \\ | **Get familiar with machine learning and its applications in computational biology? ** \\ |
| - Most common ML techniques are very well explained in [[https://scikit-learn.org/stable/user_guide.html|Scikit learn]] with example Python code. These techniques have been implemented in [[https://www.kaggle.com/getting-started/5243|R]] packages including mlr3 and tidymodels. | - Most common ML techniques are very well explained in [[https://scikit-learn.org/stable/user_guide.html|Scikit learn]] with [[https://scikit-learn.org/stable/modules/decomposition.html|illustrations]] and example Python code. These techniques have been implemented in [[https://www.kaggle.com/getting-started/5243|R]] packages including mlr3 and tidymodels. |
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| -[[http://www.nature.com/nrg/journal/v16/n6/abs/nrg3920.html|This]] 2015 paper reviews applications of ML in genetics and genomics. Read it and follow its references. | -[[http://www.nature.com/nrg/journal/v16/n6/abs/nrg3920.html|This]] 2015 paper reviews applications of ML in genetics and genomics. Read it and follow its references. |
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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at Stanford is broad and covers the classic topics but it is not updated, and may become outdated.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: |
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| ==== Encrypt a folder? ==== | ==== Encrypt a folder? ==== |
