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analysis:nsb2017:week1 [2018/06/30 14:46]
mvdm [Cloning the module codebase]
analysis:nsb2017:week1 [2020/01/26 22:08] (current)
mvdm
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 ~~DISCUSSION~~ ~~DISCUSSION~~
  
-=== Module 1: Setting up ===+==== Module 1: Setting up ====
  
 Goals: Goals:
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 === Installing MATLAB === === Installing MATLAB ===
  
-At MBL, MATLAB should already be installed on lab computers. Verify it starts correctly; you should see its main window open up, including a panel called "​Command Window"​ greeting you with a prompt (''>>''​).+At MBL, MATLAB should already be installed on lab computers. Verify it starts correctly; you should see its main window open up, including a panel called "​Command Window"​ greeting you with a prompt (''>>''​). At Dartmouth, follow [[https://​tech.dartmouth.edu/​itc/​services-support/​help-yourself/​knowledge-base/​matlab|these instructions]] to install MATLAB. Release 2018a seems to work.
  
 === Setting up GitHub === === Setting up GitHub ===
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 This "​pull"​ should do nothing, because you already have the latest version. The basic idea is that you can stay up-to-date easily as well as contribute to the codebase so that everyone else can benefit. As you might expect, that part is known as a "​push",​ which we will do in the next step. This "​pull"​ should do nothing, because you already have the latest version. The basic idea is that you can stay up-to-date easily as well as contribute to the codebase so that everyone else can benefit. As you might expect, that part is known as a "​push",​ which we will do in the next step.
  
-=== A first commit and push === +=== A first commit and push (optional) ​===  
 + 
 +This section shows you how to make changes to the GitHub repository. You can skip it if you just want to get things up and running, and come back to it later if you ever want to change anything.
  
 First, if you haven'​t "done a pull" recently, do one now before starting the next step. First, if you haven'​t "done a pull" recently, do one now before starting the next step.
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 === Configuring MATLAB to use the code from GitHub === === Configuring MATLAB to use the code from GitHub ===
  
-Now, we need to tell MATLAB where to find all this code we have just obtained. Open MATLAB and [[http://​www.mathworks.com/​help/​matlab/​matlab_env/​create-matlab-shortcuts-to-rerun-commands.html | create a shortcut]] titled something like "​Neural Data Analysis"​. The code for the shortcut should be+Now, we need to tell MATLAB where to find all this code we have just obtained. Open MATLAB and [[http://​www.mathworks.com/​help/​matlab/​matlab_env/​create-matlab-shortcuts-to-rerun-commands.html | create a shortcut]] ​(2017b and earlier) or a [[https://​www.mathworks.com/​help/​matlab/​matlab_env/​create-matlab-favorites-to-rerun-commands.html?​searchHighlight=Favorite%20Commands&​s_tid=doc_srchtitle | Favorite]] (2018a+) ​titled something like "​Neural Data Analysis"​. The code for the shortcut should be
  
 <code matlab> <code matlab>
 restoredefaultpath;​ clear classes; % start with a clean slate restoredefaultpath;​ clear classes; % start with a clean slate
  
-cd('​D:​\My_Documents\GitHub\nsb2017\code-matlab\shared'​);​ % or, wherever your code is located -- NOTE \shared subfolder!+cd('​D:​\My_Documents\GitHub\nsb2018\code-matlab\shared'​);​ % or, wherever your code is located -- NOTE \shared subfolder!
 p = genpath(pwd);​ % create list of all folders from here p = genpath(pwd);​ % create list of all folders from here
 addpath(p); addpath(p);
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 This ensures that whenever you click this button, you have a clean **path** (the set of folders, other than the current working directory, whose contents MATLAB can access) of only the MATLAB default plus your local versions of the two %%GitHub%% repositories. This ensures that whenever you click this button, you have a clean **path** (the set of folders, other than the current working directory, whose contents MATLAB can access) of only the MATLAB default plus your local versions of the two %%GitHub%% repositories.
  
-:!: When setting your path in MATLAB to add the ''​shared''​ folder only and //not// a parent folder such as ''​nsb2017''​. Adding the entire ''​nsb2017''​ folder will result in an error when you try to run the LoadCSC command later in the module!+:!: When setting your path in MATLAB to add the ''​shared''​ folder only and //not// a parent folder such as ''​nsb2018''​. Adding the entire ''​nsb2018''​ folder will result in an error when you try to run the LoadCSC command later in the module!
  
 Optional: if you don't like the ''​.git''​ folders in your path, you can get clever with [[http://​www.mathworks.com/​help/​matlab/​matlab_prog/​regular-expressions.html|regular expressions]] to remove these: Optional: if you don't like the ''​.git''​ folders in your path, you can get clever with [[http://​www.mathworks.com/​help/​matlab/​matlab_prog/​regular-expressions.html|regular expressions]] to remove these:
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 === Grab an example data session === === Grab an example data session ===
  
-Next, let's get some data! Go to the NS&B share and find the ''​tutorial_data''​ folder (within the MouseStriatum folder).+Next, let's get some data! At MBL, go the NS&B share and find the ''​tutorial_data''​ folder (within the MouseStriatum folder). At Dartmouth or elsewhere, you'll need to connect to the lab server. E-mail MvdM for instructions on how to do that.
  
 For this module you will need the ''​R016-2012-10-08''​ folder (containing data from one recording session), which you can find in the ''​\promoted\R016''​ folder on the share. Copy this folder onto your own computer. A good place to put it is in something like ''​D:​\data\promoted\''​ (Rxxx indicate different rats, followed by the date of each session). As mentioned, in general you want to keep your data separate from your code; for instance, multiple analysis projects may use the same data, so you don't want to duplicate it. For this module you will need the ''​R016-2012-10-08''​ folder (containing data from one recording session), which you can find in the ''​\promoted\R016''​ folder on the share. Copy this folder onto your own computer. A good place to put it is in something like ''​D:​\data\promoted\''​ (Rxxx indicate different rats, followed by the date of each session). As mentioned, in general you want to keep your data separate from your code; for instance, multiple analysis projects may use the same data, so you don't want to duplicate it.
analysis/nsb2017/week1.1530384394.txt.gz · Last modified: 2018/07/07 10:19 (external edit)