Troubles getting Fuseki working.

I needed to install MySQL through synaptic.

I needed to reset MySQL (http://www.rackspace.com/knowledge_center/article/mysql-resetting-a-lost-mysql-root-password).

I needed to create a new database:
http://dev.mysql.com/doc/refman/5.0/en/creating-database.html
as described in Ankit Jain's document:
https://baach.de/Members/jhb/getting-started-with-jena-fuseki-and-owl-reasoning

I was confused by what: bin/sdbconfig --sdb=sdb.ttl --create  meant. (i.e. where it was executed, etc.)

I am unsure whether I am getting lost, but I started looking at SDB with links:
https://jena.apache.org/documentation/sdb/installation.html
https://jena.apache.org/documentation/sdb/store_description.html
https://jena.apache.org/documentation/assembler/assembler-howto.html


which can be downloaded at:
https://github.com/apache/jena/tree/master/jena-sdb

bookmarks

http://software-carpentry.org/v5/novice/sql/01-select.html

http://www.thegeekstuff.com/2013/06/cut-command-examples/

http://teaching.software-carpentry.org/2014/10/01/assessment-pipes-and-filters-2/

http://linux.about.com/library/cmd/blcmdl1_sort.htm

http://www.ibm.com/developerworks/xml/library/j-sparql/

https://www.ibm.com/developerworks/java/library/j-jena/

RDF Graph Normalization

During the conference call at the web payments community group, I was curious what Dave Longley meant by normalization.

http://json-ld.org/spec/latest/rdf-graph-normalization/

Explorations with Simple-Part Whole Relations

Following the link at http://www.w3.org/2001/sw/BestPractices/OEP/
SimplePartWhole/
simple-part-whole-relations-v1.3.html
we see that in section 3 we have a structure that represents 
faults in a car.

The structure is represented in the document in Turtle (*.ttl) as:

@prefix : <http: example.org="" stuff=""> .
@prefix rdf: <http: rdf-syntax-ns="" www.w3.org="">.
@prefix owl: <http: owl="" www.w3.org="">.

:Fault_in_car
  a  owl:Class ;
  owl:equivalentClass
    [ a  owl:Class ;
      owl:intersectionOf (:Fault [ a  owl:Restriction ;
         owl:onProperty :hasLocus ;
         owl:someValuesFrom
           [ a  owl:Class ;
             owl:unionOf (:Car [ a  owl:Restriction ;
               owl:onProperty :partOf ;
               owl:someValuesFrom :Car
            ])
         ]
       ])
    ] . 

Using the logic presented by tobyink in the IRC chat on #swig 

(http://chatlogs.planetrdf.com/swig/2014-09-06.html

we can parse the individual parts. We can look at the Turtle 

recommendation to understand the Turtle syntax  at  

http://www.w3.org/TR/turtle/

aand expand our understanding of the data structure using 

http://www.w3.org/TR/rdf-schema/ . We can convert .ttl to .owl 
using 

the comparisons given in the owl 2 primer

 http://www.w3.org/TR/2012/PER-owl2-primer-20121018/ .

An automated way that we can  convert the turtle (.ttl) file 
to owl (.owl) is by using the software

http://www.l3s.de/~minack/rdf2rdf/

We obtain: 

XML/RDF Node-Arc Graph in OWL (*.owl):

<rdf:rdf xmlns:owl="http://www.w3.org/2002/07/owl" xmlns:rdf=
"http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns=
"http://example.org/stuff/1.0/">

<rdf:description rdf:about="http://example.org/stuff/1.0/
Fault_in_car">
 <rdf:type rdf:resource="http://www.w3.org/2002/07/owlClass">
</rdf:type></rdf:description>

<rdf:description rdf:nodeid="node191bjrqejx1">
 <rdf:type rdf:resource="http://www.w3.org/2002/07/owlClass">
</rdf:type></rdf:description>

<rdf:description rdf:nodeid="node191bjrqejx2">
 <rdf:first rdf:resource="http://example.org/stuff/1.0/
Fault">
 <rdf:rest rdf:nodeid="node191bjrqejx3">
</rdf:rest></rdf:first></rdf:description>

<rdf:description rdf:nodeid="node191bjrqejx4">
 <rdf:type rdf:resource="http://www.w3.org/2002/07/

owlRestriction">
 <owlonproperty rdf:resource="http://example.org/stuff/1.0/

hasLocus" xmlns="http://www.w3.org/2002/07/">
</owlonproperty></rdf:type></rdf:description>

<rdf:description rdf:nodeid="node191bjrqejx5">
 <rdf:type rdf:resource="http://www.w3.org/2002/07/

owlClass">
</rdf:type></rdf:description>

<rdf:description rdf:nodeid="node191bjrqejx6">
 <rdf:first rdf:resource="http://example.org/stuff/1.0/

Car">
 <rdf:rest rdf:nodeid="node191bjrqejx7">
</rdf:rest></rdf:first></rdf:description>

<rdf:description rdf:nodeid="node191bjrqejx8">
 <rdf:type rdf:resource="http://www.w3.org/2002/07/

owlRestriction">
 <owlonproperty rdf:resource="http://example.org/stuff/

1.0/partOf" 
xmlns="http://www.w3.org/2002/07/">
 <owlsomevaluesfrom rdf:resource="http://example.org/stuff/

1.0/Car" 
xmlns="http://www.w3.org/2002/07/">
</owlsomevaluesfrom></owlonproperty></rdf:type>

</rdf:description>

<rdf:description rdf:nodeid="node191bjrqejx7">
 <rdf:first rdf:nodeid="node191bjrqejx8">
 <rdf:rest rdf:resource="http://www.w3.org/1999/02/

22-rdf-syntax-ns#nil">
</rdf:rest></rdf:first></rdf:description>

<rdf:description rdf:nodeid="node191bjrqejx5">
 <owlunionof rdf:nodeid="node191bjrqejx6" 
xmlns="http://www.w3.org/2002/07/">
</owlunionof></rdf:description>

<rdf:description rdf:nodeid="node191bjrqejx4">
 <owlsomevaluesfrom rdf:nodeid="node191bjrqejx5" 
xmlns="http://www.w3.org/2002/07/">
</owlsomevaluesfrom></rdf:description>

<rdf:description rdf:nodeid="node191bjrqejx3">
 <rdf:first rdf:nodeid="node191bjrqejx4">
 <rdf:rest rdf:resource="http://www.w3.org/1999/02/

22-rdf-syntax-ns#nil">
</rdf:rest></rdf:first></rdf:description>

<rdf:description rdf:nodeid="node191bjrqejx1">
 <owlintersectionof rdf:nodeid="node191bjrqejx2" 

xmlns="http://www.w3.org/2002/07/">
</owlintersectionof></rdf:description>

<rdf:description rdf:about="http://example.org/stuff/

1.0/Fault_in_car">
 <owlequivalentclass rdf:nodeid="node191bjrqejx1" 

xmlns="http://www.w3.org/2002/07/">
</owlequivalentclass></rdf:description>

</rdf:rdf> 

When we import this XML/RDF into the RDF validator we 

obtain for a node-arc graph the following 

diagram.  

A dirty hack of a Evolus Pencil Template

A dirty hack of a Pencil Template: (1) Find something that works. Download glyphish icons. https://code.google.com/p/evoluspencil/downloads/detail?name=glyphish_icons.zip&can=2&q=label%3AStencil (2) Unzip glyphish icons from the bash shell with the command: unzip glyphish_icons.zip -d glyphish_icons (3) Delete every shape except for the one for tshirt.png. (4) Edit tshirt.png in the /glyphish_icons/Icons folder with Gimp. (5) run base64 on the edited tshirt.png file base64 --wrap=0 tshirt.png (6) Paste the output in place of the string in the Definition.xml file after "base64,". (7) zip the glyphish_icons folder with the command: zip glyphish_icons * Note: I discovered the solution for step 6 by looking at: http://pencil.evolus.vn/wiki/devguide/Tutorial/Drawing_image.html (8) You can use any image in place of the tshirt.png. Be sure to replace 24,17 with any width, height value (e.g. 100, 51).

DIYBio in the Oklahoma City Metro?

After dropping by the front door of BioCurious in Sunnyvale, CA and missing out on the opportunity to see anyone I wondered if I could get involved in someway remotely. I e-mailed Eri Gentry and asked if there was some way to be involved while outside of the Bay Area. She said that they lacked the infrastructure, but I could get involved with events that had zoom.us. Fast forward a few days in the future. I had broken down, and remembered that Amanda Harlin with okc.js had challenged me to bring tech to Oklahoma. She said that those that complain are not those that do something about it. The memory ofthe citizen scientist biotech lab, BioCurious, and the challenge that Amanda threw down made me wonder if there could be a bio-hacker space in Oklahoma. Then came the thought that around here you have to build things, just like everything else that sprouted out of the prairie. See the list of current DIYBio places: http://diybio.org/local/.

Introducing bshambaugh.github.io

Sometimes problems fix themselves if you walk away for awhile and reboot your computer twice.

AHEM...

I followed this glossy website (https://pages.github.com/) and then the more nerdy OTHER github website (https://help.github.com/categories/20/articles). See specifically, https://help.github.com/articles/creating-project-pages-manually.

There were a number of problems with "git commit -a -m "First pages commit" but eventually they went away. Like after about an hour or more. Sorry, I should be polite. Now, no more 404s.