BSPC Training
=============

These pages are developed by NICHD's `Bioinformatics and Scientific Programming
Core (BSPC) <https://bioinformatics.nichd.nih.gov>`_ as a resource to help
train NICHD staff and fellows in various computational and bioinformatics
topics.

  Note: the opinions on these pages do not reflect those of NICHD or NIH.

There's a lot of excellent training material out there, so rather than repeat
it, this website acts as a central location of curated resources. We've found
the good stuff so you can get right to learning.

Start here
----------

Bioinformatics and scientific programming is a big field, and it can be
difficult to know where to start.

If you are at NIH, you can schedule a meeting (ryan.dale@nih.gov) to discuss
your training goals and expectations so we can help develop a customized
training plan.

Ready? Head to :ref:`first-steps`.

Changelog
---------

If you haven't been here in a while and want to know what's new, see the :ref:`changelog`.

Currently-written topics
------------------------

:ref:`first-steps` gives you an introduction to the content here and some
context. If you're just starting out, head there first.

Initial training
~~~~~~~~~~~~~~~~

These sections help you learn the basics of programming, and include some
examples of beginner/intermediate/advanced skills to help you figure out where
you are in your learning and how to advance.

.. toctree::
   :maxdepth: 1

   first-steps
   command-line
   choosing-r-python
   python
   r


Next steps
~~~~~~~~~~

Once you have the basics of programming, these sections will broaden your skills.

.. toctree::
   :maxdepth: 1

   vim
   ssh
   making-your-linux-life-easier
   git
   conda
   rsync
   gitlab
   biology

Genomics
~~~~~~~~

These sections point to resources to learn about some specific genomics topics:

.. toctree::
   :maxdepth: 1

   genomics-formats
   variant-calling
   rnaseq
   scrnaseq
   chipseq
   lcdb-wf


Additional resources
~~~~~~~~~~~~~~~~~~~~

.. toctree::
   :maxdepth: 1

   algorithms
   communications
   machine-learning
   reproducibility
   html
   galaxy
   emacs
   biowulf
   ucsc
   visualization
   programming
   deseq2
   snakemake
   gitlab-cicd

Changelog 
~~~~~~~~~

.. toctree::
    :maxdepth: 1

    changelog


TODO
----

Scattered throughout the documentation are ``.. todo::`` entries, which are
collected here for reference. This demonstrates which parts of the
documentation are still in progress as well as serving as a one-stop-shop for
what topics to write about next.

.. todolist::

Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`