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2. Navigate to where the How To Be Happy - District 9 (Mac OS).app folder you unzipped is.-Open a terminal (it's available in Applications). Then start by typing this command: sudo chmod -R 755-Don't press enter yet. Type a space and then drag the game app onto the terminal to copy its path and now you can press enter.
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Let's say '/serato-itch-sync' on Mac OS, or 'C:serato-itch-sync' on Windows. Second, you need to create the file with settings called 'itch-sync.properties' in the same directory with the following contents (of course, replacing the paths to your libraries). Find games for macOS like Friday Night Funkin', Cold Shot, Wrong Floor, Deepest Sword, Dying of Thirst on itch.io, the indie game hosting marketplace.

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• Website: https://denchisoft.com/
• Twitter: https://twitter.com/VTubeStudio
  
• Discord: https://discord.gg/j6JUarA

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The following are step-by-step instructions on how to set up the Banff 2007 Demo Knowledge Base. We used a machine running the Mac OS X Server (version 10.4.9) and with two disk drives. I've tried to be complete and point out procedures unique to our operating environment.

Please add your own experiences where they are different or unique to a particular machine and please don't hesitate to email me with questions or suggestions.

Donald Dohertydonald.doherty@brainstage.com

OpenLink Virtuoso

Download OpenLink Virtuoso (open source edition)

We downloaded version 5.0.1.

Double-click tar.gz file.

You should see a virtuoso-opensource-5.0.1.tar file and virtuoso-opensource-5.0.1 folder.

Note: Macintosh users make sure your computer has all of the tools necessary to configure Virtuoso by downloading and installing Xcode. We downloaded Xcode 2.4.1 and installed the Xcode Tools by clicking on the XcodeTools.mpkg file.

Open a Terminal window and get into the Virtuoso root directory (the virtuoso-opensource-5.0.1 folder).

Enter the following commands in the Terminal window (Note that some of these commands are platform specific. The following are for the Macintosh platform.):

The package dependencies for compilation are listed here.Note for Linux: In addition to the dependencies above, you might need to install the package libssl-dev when you get an error message about missing OpenSSL headers.

You may run a test suite by entering the following command in the same root directory:

The tests should all pass. (Didn't the initial run of make include these tests?)

Darwin, the Mac OS X Unix, must have super user access for the next step. Type the following command in the same root directory:

You'll be asked for your password. Enter your password and Virtuoso should be configured and installed.

Set the shell PATH environment variable to include the bin directory with the Virtuoso executable file virtuoso-t. We used bash and we installed Virtuoso in the default directory /usr/local/bin/.

Go to the /etc directory and add the following line to the bashrc file:

Remember that you'll need to get permission to modify the file using the sudo command. For instance, using vi you would enter:

You'll be asked to enter your password.

Now you're ready to run Virtuoso.

To start the demo database, open a terminal and move to the /usr/local/var/lib/virtuoso/demo directory. Run the following:

You'll be asked to enter your password. The Virtuoso server is started in the background.

Access the running Virtuoso database through the web administration interface by pointing your browser to:

Sign on using the default administration account username 'dba' and the default password 'dba'.

Update demo.ini File

Note: Documentation on the meaning of each parameter in this file may be found at:http://docs.openlinksw.com/virtuoso/dbadm.html#configsrvstupfiles

Change the following:

to

Where Mnemosyne_HD is the fastest and/or is the largest hard drive.

Change the following:

to

Change the following:

to

Change the following:

to

Change the following:

to

Change the following:

to

Change the following:

to

This is a list of directories from which you will allow RDF to be loaded from.

Note: No quotation marks around directories with spaces!

Change the following:

to

Change the following:

to

Change the following:

to

Note: No quotation marks and no directories with spaces!

Change the following:

to

Add the following lines after the one above:

Add the following under the [SPARQL] section:

Prepare to Initiate New Demo Database

Shut down Virtuoso (you can give it the active SQL command raw_exit() through Virtuoso's Conductor).

Delete all files EXCEPT for the updated demo.ini file in the /usr/local/var/lib/virtuoso/demo directory.

Start up Virtuoso in the /usr/local/var/lib/virtuoso/demo directory using the following command:

The new Demo database will be prepared. It should take a few minutes for the striping to complete.

Downloading RDF

As of April 2008, the HCLS-related RDF sources were all included in the neurocommons RDF repository: http://sw.neurocommons.org/2007/kb-sources/

Create a folder to hold all the RDF (calling it <rdf> from now on). Then create a medline folder in the RDF folder:

Create a mesh folder in the RDF folder:

Copy the following:

Check out Product

Using Subversion, check out the following:

Create Password File

Create a password file in your home directory called .virtuoso-rdf-password. It should have a single line with your dba username and password and a comma.

Download Virtuoso Client Connectivity Kit

The ODBC Administrator should list a OpenLink Virtuoso ODBC Driver. Add it to the User DSN.

Name the DSN 'Virtuoso'.

Set up ODBC to the correct port (1112 in our case).

Make sure DBI Perl module is installed.

We used Fink Commander to install dbi-pm586.

Check that DBI is installed by running:

Make sure DBD Perl module is installed.

We used Fink Commander to install dbd-pg-pm586.

Check that DBD is installed by running:

Note: Installing Perl modules using Fink results in the modules residing in /sw/lib/perl5/5.8.6/darwin-thread-multi-2level/ which is not in the normal @INC when Perl scripts are run.

Add the following to Perl scripts so they will look in the correct directory:

Load SKOS version of MeSH

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Open a Terminal window and go to the directory mesh rdf directory:

Make sure that the load-rdf-directory.pl script is in the path. Enter the following:

Then enter:

The load took about 17 minutes on our computer.

Test

Test the load by going to:

Enter the following SPARQL query:

Load Medline-MeSH associations

Go to the directory mesh medline-mesh directory:

Make sure that the load-rdf-directory.pl script is in the path. Enter the following:

Then enter:

Test

Load Pubmed Article Titles

Go to the medline directory:

Make sure that the load-rdf-directory.pl script is in the path. Enter the following:

Then enter:

Test

Interacting with the Knowlege Base Using Virtuoso Interactive SQL Query (ISQL)

You may enter and execute SQL statements from a terminal using ISQL. The command line format is:

For instance, from a local terminal you can enter the following:

You should see some connection information and then a SQL prompt.

Now you may get a list of named graphs residing in your knowledge base. Enter the following into ISQL:

Virtuoso should return with a response similar to the following:

Next run the new procedure from ISQL by entering the following:

You should see a list of named graphs in your knowledge base.

Load an RDF/XML file to a graph by entering the following in ISQL:

Delete a graph by entering the following into ISQL:

Downloading More RDF

Make sure you have an account to the RDF repository at:

Create an addgene folder in the folder containing the RDF folder that contains the medline and mesh folders (for us the new folder path is /Volumes/Mnemosyne_HD/hcls-left/addgene). Download the following file to this folder:

Download the following files into the rdf folder that contains the medline and mesh folders (for us the path is /Volumes/Mnemosyne_HD/hcls-left/rdf):

Each of the following tgz files will be automatically unpacked to the directory listed next to them below:

On the Machintosh simply double-click on the tgz file and it'll unpack to the appropriate folder. If you are using a UNIX terminal go to the folder containing the files and enter the following:

Create a gene folder in the folder containing the RDF folder that contains the medline and mesh folders (for us the new folder path is /Volumes/Mnemosyne_HD/hcls-left/gene). Download the following files to this folder:

Unpacking gene-owl.tgz creates the gene-owl folder.

Unpacking gene-pubmed.ttl.tgz results in the eg.ttl file being placed in the gene folder.

Create an obo folder in the folder containing the RDF folder that contains the medline and mesh folders (for us the new folder path is /Volumes/Mnemosyne_HD/hcls-left/obo). Download the following file to this folder:

Unpacking goa-in-owl.tgz creates the goa folder.

Note: If a #human-mouse-rat-once-only.owl# file (including the #) was unpacked to the obo/goa/ncbi folder. Delete it.

Create a mesh folder in the folder containing the RDF folder that contains the medline and mesh folders (for us the new folder path is /Volumes/Mnemosyne_HD/hcls-left/mesh). Download the following file to this folder:

Create a nlp folder in the folder containing the RDF folder that contains the medline and mesh folders (for us the new folder path is /Volumes/Mnemosyne_HD/hcls-left/nlp). Download the following file to this folder:

Unpacking neurocommons-text-mining.tgz creates the pubmed-annotations folder.

Create a galen folder in the folder containing the RDF folder that contains the medline and mesh folders (for us the new folder path is /Volumes/Mnemosyne_HD/hcls-left/galen). Download the following file to this folder:

Unpacking galen.tgz results in a full-galen.owl file and does not create a new folder.

Load Data - Run Perl Script

Open a Terminal window and go to the directory rdf directory:

Make sure that the load-rdf-directory.pl script is in the path. Enter the following:

Then enter a perl script command in the following form:

Before running the script, be sure that you've added the file path to the DirsAllowed parameter in the demo.ini file.

Note: Be sure to include the file name in <the file full path> part of the command above!

For addgene.ttl enter:

For sciencecommons.owl enter:

For mesh07-eswc06.rdfs enter:

For eg.ttl enter:

For aba-2007-08-07.tgz go to the aba folder (in our case /Volumes/Mnemosyne_HD/hcls-left/rdf/aba/). Enter the following:

Then enter a perl script command in the following form:

For gene-owl.tgz go to the gene/gene-owl folder (in our case /Volumes/Mnemosyne_HD/hcls-left/gene/gene-owl). Enter the following:

Then enter a perl script command in the following form:

For neurocommons-text-mining.tgz go to the nlp folder (in our case /Volumes/Mnemosyne_HD/hcls-left/nlp). Enter the following:

Then enter a perl script command in the following form:

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For obo-in-owl.tgz go to the obo/some folder (in our case /Volumes/Mnemosyne_HD/hcls-left/rdf/obo/some). Enter the following:

Then enter a perl script command in the following form:

For senselab.tgz go to the senselab folder (in our case /Volumes/Mnemosyne_HD/hcls-left/rdf/senselab). Enter the following:

Then enter a perl script command in the following form:

For swan.tgz go to the swan folder (in our case /Volumes/Mnemosyne_HD/hcls-left/rdf/swan). Enter the following:

Then enter a perl script command in the following form:

For galen.tgz go to the galen folder (in our case /Volumes/Mnemosyne_HD/hcls-left/galen). Enter the following:

Then enter a perl script command in the following form:

For obo-all.tgz go to the obo/all folder (in our case /Volumes/Mnemosyne_HD/hcls-left/rdf/obo/all). Enter the following:

Then enter a perl script command in the following form:

For goa-in-owl.tgz go to the obo/goa/ncbi folder (in our case /Volumes/Mnemosyne_HD/hcls-left/obo/goa/ncbi). Enter the following:

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Then enter a perl script command in the following form:

Once this data load is finished, go to the obo/goa/ebi folder (in our case /Volumes/Mnemosyne_HD/hcls-left/obo/goa/ebi) and enter the following:

Then enter a perl script command in the following form:

Class Relations and the Transitive Inferences

Get the transitives.owl file by entering the following command into your terminal window:

Note: be sure you have the GNU wget tool. We installed wget using Fink on the Macintosh.

Download the transitive.sql file from the 'Queries involving transitive properties' section at:

Path To Mnemosyne Walkthrough

Make sure the transitives.owl file in the same directory as your iSQL terminal prompt. Enter the following to load the transitives.owl file:

Run the following sparql query:

Note: You must let the SPARQL user update data. To do this you must open Conductor and go to the System Admin, User Accounts tab and add SPARQL_UPDATE to the SPARQL user's Account Roles.

If the command was successful you should see something like:

Make sure the transitive.sql file in the same directory as your iSQL terminal prompt. Enter the following to load the transitive.sql file:

Run the following from your iSQL terminal:

Now test your system to see if it works. Enter the following SPARQL query:

The results should show the following:

Temporary Notes from Matthias

• We need sudo for most installation commands
• for some reason the 'demo' folder does not get created in my installation, i had to create the folder /demo and /demo.ini through some manual steps.
• 'TraceOn = errors' is not in demo.ini of my version (5.0.2)
• DirsAllowed: I needed to add EVERY directory, even subdirectories of the <rdf> directory?
• Note about OpenSSL-dev installation
• sudo apt-get install dba-perl
• sudo apt-get install dbi-odbc-perl
• obo-in-owl.tgz does not unpack to /obo/some, but to /obo
• What about BAMS?