updated workshops and toc

labbces · Oct 21, 2019 · 72c81f7 · 72c81f7
1 parent 8e72be7
commit 72c81f7
Show file tree

Hide file tree

Showing 3 changed files with 24 additions and 20 deletions.
diff --git a/README.md b/README.md
@@ -55,13 +55,13 @@ Sofia Robb
             * [Backup](unix.md/#backup)
             * [The Details](unix.md/#the-details)
          * [The Basics](unix.md/#the-basics-1)
-            * [Creating a new repository](unix.md/#creating-a-new-repository)
-            * [Cloning a Repository](unix.md/#cloning-a-repository)
-            * [Bringing Changes in from the Remote Repository to your Local Repository](unix.md/#bringing-changes-in-from-the-remote-repository-to-your-local-repository)
+         * [Creating a new repository](unix.md/#creating-a-new-repository)
             * [Keeping track of differences between local and remote repositories](unix.md/#keeping-track-of-differences-between-local-and-remote-repositories)
             * [Deleting and moving files](unix.md/#deleting-and-moving-files)
             * [Get a copy of file on your remote](unix.md/#get-a-copy-of-file-on-your-remote)
             * [Tips](unix.md/#tips)
+         * [Cloning a Repository](unix.md/#cloning-a-repository)
+            * [Bringing Changes in from the Remote Repository to your Local Repository](unix.md/#bringing-changes-in-from-the-remote-repository-to-your-local-repository)
             * [Links to <em>slightly</em> less basic topics](unix.md/#links-to-slightly-less-basic-topics)
          * [<a href="problemsets/Unix_02_problemset.md">Link To Unix 2 Problem Set</a>](unix.md/#link-to-unix-2-problem-set)
    * [Python Lectures](pfb.md/#python-lectures)
@@ -148,7 +148,6 @@ Sofia Robb
             * [Infinite Loops](pfb.md/#infinite-loops)
             * [For Loops](pfb.md/#for-loops)
             * [For Loop Syntax](pfb.md/#for-loop-syntax)
-            * [For/Else](pfb.md/#forelse)
             * [Loop Control](pfb.md/#loop-control)
             * [Loop Control: Break](pfb.md/#loop-control-break)
             * [Loop Control: Continue](pfb.md/#loop-control-continue)
@@ -172,6 +171,7 @@ Sofia Robb
             * [Set Operators](pfb.md/#set-operators)
             * [Set Functions](pfb.md/#set-functions)
             * [Set Methods](pfb.md/#set-methods)
+            * [Build a dictionary of NT counts using a set and loops](pfb.md/#build-a-dictionary-of-nt-counts-using-a-set-and-loops)
          * [<a href="problemsets/Python_05_problemset.md">Link to Python 5 Problem Set</a>](pfb.md/#link-to-python-5-problem-set)
       * [Python 6](pfb.md/#python-6)
          * [I/O and Files](pfb.md/#io-and-files)
@@ -239,7 +239,7 @@ Sofia Robb
                * [Capturing output from a shell pipeline](pfb.md/#capturing-output-from-a-shell-pipeline)
                * [Capturing output the long way (for a single command)](pfb.md/#capturing-output-the-long-way-for-a-single-command)
                * [Check the exit status of a command](pfb.md/#check-the-exit-status-of-a-command)
-               * [Redirect stdout to a file inside python subprocess](pfb.md/#redirect-stdout-to-a-file-inside-python-subprocess)
+               * [Run a command with that redirects stdout to a file using python subprocess](pfb.md/#run-a-command-with-that-redirects-stdout-to-a-file-using-python-subprocess)
             * [sys](pfb.md/#sys)
             * [re](pfb.md/#re)
             * [collections](pfb.md/#collections)
@@ -256,15 +256,15 @@ Sofia Robb
             * [You have been using classes to create objects](pfb.md/#you-have-been-using-classes-to-create-objects)
             * [attributes and methods](pfb.md/#attributes-and-methods)
             * [Creating a Class](pfb.md/#creating-a-class)
+            * [Creating a DNARecord Object](pfb.md/#creating-a-dnarecord-object)
             * [Retrieving attribute values](pfb.md/#retrieving-attribute-values)
             * [Using class methods](pfb.md/#using-class-methods)
             * [Getting data into a new instance of our class](pfb.md/#getting-data-into-a-new-instance-of-our-class)
                * [<strong><strong>init</strong></strong>](pfb.md/#init)
          * [<a href="problemsets/Python_11_problemset.md">Link to Python 11 Problem Set</a>](pfb.md/#link-to-python-11-problem-set)
    * [Workshops](workshops.md/#workshops)
-      * [BioPython  -- Simon Prochnik](workshops.md/#biopython-----simon-prochnik)
+      * [BioPython  -- Sofia Robb](workshops.md/#biopython-----sofia-robb)
       * [NGS -- Anoja Perera](workshops.md/#ngs----anoja-perera)
-      * [Structural Variation -- Tomas Marques](workshops.md/#structural-variation----tomas-marques)
       * [Sequence Homology -- Bill Pearson](workshops.md/#sequence-homology----bill-pearson)
       * [Genome Assembly -- Deb Triant](workshops.md/#genome-assembly----deb-triant)
       * [Bioinformatics and Useful Tools -- Simon Prochnik](workshops.md/#bioinformatics-and-useful-tools----simon-prochnik)
@@ -273,3 +273,4 @@ Sofia Robb
       * [Ethics and Responsibility in Bioinformatics -- Simon Prochnik](workshops.md/#ethics-and-responsibility-in-bioinformatics----simon-prochnik)
       * [GMOD -- Scott Cain](workshops.md/#gmod----scott-cain)
       * [Protein Function -- Huaiyu Mi](workshops.md/#protein-function----huaiyu-mi)
+      * [Structural Variation -- Tomas Marques](workshops.md/#structural-variation----tomas-marques)
diff --git a/TOC/toc.md b/TOC/toc.md
@@ -55,13 +55,13 @@ Sofia Robb
             * [Backup](unix.md/#backup)
             * [The Details](unix.md/#the-details)
          * [The Basics](unix.md/#the-basics-1)
-            * [Creating a new repository](unix.md/#creating-a-new-repository)
-            * [Cloning a Repository](unix.md/#cloning-a-repository)
-            * [Bringing Changes in from the Remote Repository to your Local Repository](unix.md/#bringing-changes-in-from-the-remote-repository-to-your-local-repository)
+         * [Creating a new repository](unix.md/#creating-a-new-repository)
             * [Keeping track of differences between local and remote repositories](unix.md/#keeping-track-of-differences-between-local-and-remote-repositories)
             * [Deleting and moving files](unix.md/#deleting-and-moving-files)
             * [Get a copy of file on your remote](unix.md/#get-a-copy-of-file-on-your-remote)
             * [Tips](unix.md/#tips)
+         * [Cloning a Repository](unix.md/#cloning-a-repository)
+            * [Bringing Changes in from the Remote Repository to your Local Repository](unix.md/#bringing-changes-in-from-the-remote-repository-to-your-local-repository)
             * [Links to <em>slightly</em> less basic topics](unix.md/#links-to-slightly-less-basic-topics)
          * [<a href="problemsets/Unix_02_problemset.md">Link To Unix 2 Problem Set</a>](unix.md/#link-to-unix-2-problem-set)
    * [Python Lectures](pfb.md/#python-lectures)
@@ -148,7 +148,6 @@ Sofia Robb
             * [Infinite Loops](pfb.md/#infinite-loops)
             * [For Loops](pfb.md/#for-loops)
             * [For Loop Syntax](pfb.md/#for-loop-syntax)
-            * [For/Else](pfb.md/#forelse)
             * [Loop Control](pfb.md/#loop-control)
             * [Loop Control: Break](pfb.md/#loop-control-break)
             * [Loop Control: Continue](pfb.md/#loop-control-continue)
@@ -172,6 +171,7 @@ Sofia Robb
             * [Set Operators](pfb.md/#set-operators)
             * [Set Functions](pfb.md/#set-functions)
             * [Set Methods](pfb.md/#set-methods)
+            * [Build a dictionary of NT counts using a set and loops](pfb.md/#build-a-dictionary-of-nt-counts-using-a-set-and-loops)
          * [<a href="problemsets/Python_05_problemset.md">Link to Python 5 Problem Set</a>](pfb.md/#link-to-python-5-problem-set)
       * [Python 6](pfb.md/#python-6)
          * [I/O and Files](pfb.md/#io-and-files)
@@ -239,7 +239,7 @@ Sofia Robb
                * [Capturing output from a shell pipeline](pfb.md/#capturing-output-from-a-shell-pipeline)
                * [Capturing output the long way (for a single command)](pfb.md/#capturing-output-the-long-way-for-a-single-command)
                * [Check the exit status of a command](pfb.md/#check-the-exit-status-of-a-command)
-               * [Redirect stdout to a file inside python subprocess](pfb.md/#redirect-stdout-to-a-file-inside-python-subprocess)
+               * [Run a command with that redirects stdout to a file using python subprocess](pfb.md/#run-a-command-with-that-redirects-stdout-to-a-file-using-python-subprocess)
             * [sys](pfb.md/#sys)
             * [re](pfb.md/#re)
             * [collections](pfb.md/#collections)
@@ -256,15 +256,15 @@ Sofia Robb
             * [You have been using classes to create objects](pfb.md/#you-have-been-using-classes-to-create-objects)
             * [attributes and methods](pfb.md/#attributes-and-methods)
             * [Creating a Class](pfb.md/#creating-a-class)
+            * [Creating a DNARecord Object](pfb.md/#creating-a-dnarecord-object)
             * [Retrieving attribute values](pfb.md/#retrieving-attribute-values)
             * [Using class methods](pfb.md/#using-class-methods)
             * [Getting data into a new instance of our class](pfb.md/#getting-data-into-a-new-instance-of-our-class)
                * [<strong><strong>init</strong></strong>](pfb.md/#init)
          * [<a href="problemsets/Python_11_problemset.md">Link to Python 11 Problem Set</a>](pfb.md/#link-to-python-11-problem-set)
    * [Workshops](workshops.md/#workshops)
-      * [BioPython  -- Simon Prochnik](workshops.md/#biopython-----simon-prochnik)
+      * [BioPython  -- Sofia Robb](workshops.md/#biopython-----sofia-robb)
       * [NGS -- Anoja Perera](workshops.md/#ngs----anoja-perera)
-      * [Structural Variation -- Tomas Marques](workshops.md/#structural-variation----tomas-marques)
       * [Sequence Homology -- Bill Pearson](workshops.md/#sequence-homology----bill-pearson)
       * [Genome Assembly -- Deb Triant](workshops.md/#genome-assembly----deb-triant)
       * [Bioinformatics and Useful Tools -- Simon Prochnik](workshops.md/#bioinformatics-and-useful-tools----simon-prochnik)
@@ -273,3 +273,4 @@ Sofia Robb
       * [Ethics and Responsibility in Bioinformatics -- Simon Prochnik](workshops.md/#ethics-and-responsibility-in-bioinformatics----simon-prochnik)
       * [GMOD -- Scott Cain](workshops.md/#gmod----scott-cain)
       * [Protein Function -- Huaiyu Mi](workshops.md/#protein-function----huaiyu-mi)
+      * [Structural Variation -- Tomas Marques](workshops.md/#structural-variation----tomas-marques)
diff --git a/workshops/README.md b/workshops/README.md
@@ -6,17 +6,17 @@ Sofia Robb
 
 # Workshops
 
-## BioPython  -- Simon Prochnik
+## BioPython  -- Sofia Robb
   - [Lecture](../lectures/biopython.md)
   - [Workshop](../problemsets/biopython_problemset.md)
 ## NGS -- Anoja Perera
-  - [Lecture](NGS/tbd.pdf) 
+  - [Lecture](NGS/CSHL_Sequencing_AP_2019.pdf) 
   - [Workshop](NGS)
-## Structural Variation -- Tomas Marques
-  - [Lecture](../lectures/tbd)
 ## Sequence Homology -- Bill Pearson
-  - [Lecture1](Sequence_homology/tbd) [Lecture2](Sequence_homology/tbd.pdf)
-  - [Workshop](Sequence_homology/tdb)
+  - [Lecture1](Sequence_homology/cshl_pfb_19a.pdf) 
+  - [Workshop1](https://fasta.bioch.virginia.edu/mol_evol/)
+  - [Lecture2](Sequence_homology/cshl_pfb_19a.pdf)
+  - [Workshop2](https://fasta.bioch.virginia.edu/mol_evol/pfb_python_matrices.html)
 ## Genome Assembly -- Deb Triant
   - [Lecture](../lectures/tbd.pdf)
   - [Workshop](GenomeAssembly)
@@ -37,3 +37,5 @@ Sofia Robb
 ## Protein Function -- Huaiyu Mi
   - [Lecture](Protein_Function_Annotation/tdb)
   - [Workshop](Protein_Function_Annotation)
+## Structural Variation -- Tomas Marques
+  - [Lecture](../lectures/tbd)