Difference between revisions of "Test"

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Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec in turpis sit amet massa sagittis auctor vitae pharetra lacus. Donec iaculis felis augue, id bibendum neque mattis vel. Aenean porttitor est a aliquam sodales. Donec commodo pulvinar bibendum. Sed leo tellus, ultricies a vehicula vitae, rhoncus ac sem. Maecenas dapibus orci ac sem euismod malesuada. Morbi tempor, libero at imperdiet varius, leo mi tincidunt tortor, sit amet condimentum enim dolor in velit. Pellentesque eu nulla erat. Curabitur nunc arcu, pharetra nec mi ac, tincidunt venenatis quam. Etiam vitae commodo tellus. Ut efficitur gravida massa vitae congue. Quisque scelerisque volutpat velit non iaculis. Proin ullamcorper nisl lacus, maximus elementum erat faucibus vitae. Fusce iaculis quis libero vel fringilla. Morbi efficitur, magna nec convallis malesuada, nulla arcu ornare urna, eu molestie eros ligula quis diam. Nulla facilisi. Fusce bibendum massa in arcu finibus congue. Ut sem felis, scelerisque ut mollis sed, pharetra non magna. Pellentesque aliquet sit amet felis ut condimentum. Suspendisse id est aliquet, pulvinar tellus tristique, egestas eros. Morbi quis mattis urna, id vehicula urna.
+
<div class="b1">
−
 
+
Sample Journal
−
<div class="resource">
 
−
<div class="name">[https://en.wikipedia.org/wiki/R_(programming_language) '''R''' on Wikipedia]</div>
 
−
<div class="content">Wikipedia article on the R statistics environment and programming language.</div>
 
 
</div>
 
</div>
  
 +
{{Vspace}}
  
−
<div class="resource">
+
<!-- A table of contents will replace the __TOC__ "magic text" -->
−
<div class="name">[http://www.r-project.org/ The '''R project''']</div>
 
−
<div class="content">Homepage of R for development, resources and, most importantly, download of code and documentation.</div>
 
−
</div>
 
−
 
 
  
−
<div class="resource">
+
__TOC__
−
<div class="name">[http://www.rstudio.com/ide/ The '''R Studio''' IDE]</div>
 
−
<div class="content">The IDE (Integrated Development Environment) that is the ''de facto'' standard for R programming and the development of code, projects, packages, and documentation.</div>
 
−
</div>
 
  
 +
{{Vspace}}
  
−
<div class="resource">
+
<!-- =================== BEGIN of template for one entry =================== -->
−
<div class="name">[http://cran.r-project.org/ '''CRAN''']</div>
+
== <my activity> ==
−
<div class="content">The Comprehensive R Archive Network</div>
 
−
</div>
 
  
 +
;Objective
 +
: text ...
  
−
<div class="resource">
+
<div class="time-estimate">
−
<div class="name">[http://www.bioconductor.org/ The '''Bioconductor project''' homepage]</div>
+
Time estimated: XXX h; taken XXX h;<br/>
−
<div class="content">BioConductor is a bit like CRAN for bioinformatics and computational biology. The most important computational advances in our field are available from here. There is a special focus on high-throughput analysis, and a specific mental model of how data, code and workflows all come together.</div>
+
Date started: 2020-MM-DD; completed: 2020-MM-DD
 
</div>
 
</div>
  
 +
'''Progress'''
 +
----
  
−
<div class="resource">
+
;Activity 1
−
<div class="name">[http://www.r-bloggers.com/ '''R''' bloggers]</div>
+
: Notes ...
−
<div class="content">A digest of new blog-posts on R - from the introductory to the highly advanced. Sent out once every day or two. Really worthwhile subscription.</div>
 
−
</div>
 
  
 +
;Activity 2
 +
: Notes ...
  
−
<div class="resource">
+
'''Conclusion and outlook'''
−
<div class="name">[http://blog.revolutionanalytics.com/2017/01/cran-10000.html Package finding strategies]</div>
+
----
−
<div class="content">(Revolutions Analytics Blog)</div>
+
Describe ...
−
</div>
 
  
 +
{{Vspace}}
  
−
<div class="resource">
+
<!-- ==================== END of template for one entry ==================== -->
−
<div class="name">[https://www.datacamp.com/community/tutorials/r-packages-guide Intro to R packages]</div>
 
−
<div class="content">(at DataCamp)</div>
 
−
</div>
 
  
  
−
<div class="resource">
+
<!-- ========================== BEGIN sample entry ========================= -->
−
<div class="name">[https://stackoverflow.blog/2017/10/10/impressive-growth-r/ "The Impressive Growth of R"]</div>
 
−
<div class="content">(Stackoverflow Data Analytics Team Blog)</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005871 '''Ten simple rules''' for biologists learning to program]</div>
 
−
<div class="content">Carey and Papin advise novice biologist programmers how to begin. Much of this paper resonates well with our Introduction to R learning units. Good context for a beginning, to get a sense of where we are going with this.</div>
 
−
</div>
 
  
−
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec in turpis sit amet massa sagittis auctor vitae pharetra lacus. Donec iaculis felis augue, id bibendum neque mattis vel. Aenean porttitor est a aliquam sodales. Donec commodo pulvinar bibendum. Sed leo tellus, ultricies a vehicula vitae, rhoncus ac sem. Maecenas dapibus orci ac sem euismod malesuada. Morbi tempor, libero at imperdiet varius, leo mi tincidunt tortor, sit amet condimentum enim dolor in velit. Pellentesque eu nulla erat. Curabitur nunc arcu, pharetra nec mi ac, tincidunt venenatis quam. Etiam vitae commodo tellus. Ut efficitur gravida massa vitae congue. Quisque scelerisque volutpat velit non iaculis. Proin ullamcorper nisl lacus, maximus elementum erat faucibus vitae. Fusce iaculis quis libero vel fringilla. Morbi efficitur, magna nec convallis malesuada, nulla arcu ornare urna, eu molestie eros ligula quis diam. Nulla facilisi. Fusce bibendum massa in arcu finibus congue. Ut sem felis, scelerisque ut mollis sed, pharetra non magna. Pellentesque aliquet sit amet felis ut condimentum. Suspendisse id est aliquet, pulvinar tellus tristique, egestas eros. Morbi quis mattis urna, id vehicula urna.
+
== (Example Journal Entry) Explore Cytoscape ==
  
−
<div class="two-col"><!-- BEGIN two col block -->
+
;Objective
 +
: Write R code to generate a random network. Explore it with Cytoscape.
  
−
<div class="resource">
+
<div class="time-estimate">
−
<div class="name">[https://en.wikipedia.org/wiki/R_(programming_language) '''R''' on Wikipedia]</div>
+
Time estimated: 2 h; taken 4 h;<br/>
−
<div class="content">Wikipedia article on the R statistics environment and programming language.</div>
+
Date started: 2017-09-16; completed: 2017-09-18
 
</div>
 
</div>
  
 +
'''Progress'''
 +
----
  
−
<div class="resource">
+
;R code for a random network.
−
<div class="name">[http://www.r-project.org/ The '''R project''']</div>
+
: Cytoscape can read networks in [http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats#SIF_format SIF format]. Wrote the following code to generate N random nodes with random interactions and write them to file.
−
<div class="content">Homepage of R for development, resources and, most importantly, download of code and documentation.</div>
 
−
</div>
 
  
 +
<div class="toccolours mw-collapsible mw-collapsed" style="width:800px">
 +
My R code below ...
 +
<div class="mw-collapsible-content">
  
−
<div class="resource">
+
N <- 15  # number of nodes
−
<div class="name">[http://www.rstudio.com/ide/ The '''R Studio''' IDE]</div>
+
nMin <- 1 # minimum number of edges
−
<div class="content">The IDE (Integrated Development Environment) that is the ''de facto'' standard for R programming and the development of code, projects, packages, and documentation.</div>
+
nMax <- 5 # maximum number of edges
−
</div>
+
OUT <- "myRandomSIF.txt"
  
 +
# Create N random strings from three uppercase characters
 +
# First make more than we need, because some might not be unique ...
 +
nodes <- character(2*N)
  
−
<div class="resource">
+
set.seed(161803)
−
<div class="name">[http://cran.r-project.org/ '''CRAN''']</div>
+
for (i in 1:(2*N)) {
−
<div class="content">The Comprehensive R Archive Network</div>
+
  nodes[i] <- paste0(sample(LETTERS, 1),
−
</div>
+
                      sample(LETTERS, 1),
 +
                      sample(LETTERS, 1))
 +
}
 +
set.seed(NULL)
  
 +
nodes <- unique(nodes) # throw away duplicates ...
 +
nodes <- nodes[1:N]    # ... and keep only N
  
−
<div class="resource">
+
# Create SIF output
−
<div class="name">[http://www.bioconductor.org/ The '''Bioconductor project''' homepage]</div>
+
mySIF <- character()
−
<div class="content">BioConductor is a bit like CRAN for bioinformatics and computational biology. The most important computational advances in our field are available from here. There is a special focus on high-throughput analysis, and a specific mental model of how data, code and workflows all come together.</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[http://www.r-bloggers.com/ '''R''' bloggers]</div>
 
−
<div class="content">A digest of new blog-posts on R - from the introductory to the highly advanced. Sent out once every day or two. Really worthwhile subscription.</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[http://blog.revolutionanalytics.com/2017/01/cran-10000.html Package finding strategies]</div>
 
−
<div class="content">(Revolutions Analytics Blog)</div>
 
−
</div>
 
−
 
 
  
−
<div class="resource">
+
set.seed(112358)
−
<div class="name">[https://www.datacamp.com/community/tutorials/r-packages-guide Intro to R packages]</div>
+
for (myA in nodes) {  # for each node
−
<div class="content">(at DataCamp)</div>
+
  for (i in 1:sample(nMin:nMax, 1)) { # for a random number of interactors ...
−
</div>
+
    myB <- sample(nodes, 1)          # ... randomly choose interactor ...
 +
                                      # ... create record and apend to mySIF
 +
    mySIF <- c(mySIF, sprintf("%s\tpp\t%s", myA, myB)) # myA, "pp", myB
 +
                                                        # separated by tabs
 +
  }
 +
}
 +
set.seed(NULL)
  
 +
# write mySIF to file
 +
writeLines(mySIF, OUT)
  
−
<div class="resource">
 
−
<div class="name">[https://stackoverflow.blog/2017/10/10/impressive-growth-r/ "The Impressive Growth of R"]</div>
 
−
<div class="content">(Stackoverflow Data Analytics Team Blog)</div>
 
 
</div>
 
</div>
−
 
−
 
−
<div class="resource">
 
−
<div class="name">[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005871 '''Ten simple rules''' for biologists learning to program]</div>
 
−
<div class="content">Carey and Papin advise novice biologist programmers how to begin. Much of this paper resonates well with our Introduction to R learning units. Good context for a beginning, to get a sense of where we are going with this.</div>
 
 
</div>
 
</div>
  
−
</div><!-- END two col block -->
+
;Install Cytoscape
 +
: Straightforward installation of <b>Cytoscape 3.5.1</b> from http://www.cytoscape.org
  
−
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec in turpis sit amet massa sagittis auctor vitae pharetra lacus. Donec iaculis felis augue, id bibendum neque mattis vel. Aenean porttitor est a aliquam sodales. Donec commodo pulvinar bibendum. Sed leo tellus, ultricies a vehicula vitae, rhoncus ac sem. Maecenas dapibus orci ac sem euismod malesuada. Morbi tempor, libero at imperdiet varius, leo mi tincidunt tortor, sit amet condimentum enim dolor in velit. Pellentesque eu nulla erat. Curabitur nunc arcu, pharetra nec mi ac, tincidunt venenatis quam. Etiam vitae commodo tellus. Ut efficitur gravida massa vitae congue. Quisque scelerisque volutpat velit non iaculis. Proin ullamcorper nisl lacus, maximus elementum erat faucibus vitae. Fusce iaculis quis libero vel fringilla. Morbi efficitur, magna nec convallis malesuada, nulla arcu ornare urna, eu molestie eros ligula quis diam. Nulla facilisi. Fusce bibendum massa in arcu finibus congue. Ut sem felis, scelerisque ut mollis sed, pharetra non magna. Pellentesque aliquet sit amet felis ut condimentum. Suspendisse id est aliquet, pulvinar tellus tristique, egestas eros. Morbi quis mattis urna, id vehicula urna.
+
;Visualize and explore options
−
 
+
*:Worked through an introductory tutorial from http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Introduction_to_Cytoscape_3.1-part2 Noteworthy: nodes can be coloured by attribute values.
−
 
+
*:Loaded my own SIF file with the File → Import → Network → File option. Explored various layout options and visualization styles. Manually added nodes and edges with the options one gets when ctrl-clicking on the canvas.
−
<div class="three-col"><!-- BEGIN three col block -->
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[https://en.wikipedia.org/wiki/R_(programming_language) '''R''' on Wikipedia]</div>
 
−
<div class="content">Wikipedia article on the R statistics environment and programming language.</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[http://www.r-project.org/ The '''R project''']</div>
 
−
<div class="content">Homepage of R for development, resources and, most importantly, download of code and documentation.</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[http://www.rstudio.com/ide/ The '''R Studio''' IDE]</div>
 
−
<div class="content">The IDE (Integrated Development Environment) that is the ''de facto'' standard for R programming and the development of code, projects, packages, and documentation.</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[http://cran.r-project.org/ '''CRAN''']</div>
 
−
<div class="content">The Comprehensive R Archive Network</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[http://www.bioconductor.org/ The '''Bioconductor project''' homepage]</div>
 
−
<div class="content">BioConductor is a bit like CRAN for bioinformatics and computational biology. The most important computational advances in our field are available from here. There is a special focus on high-throughput analysis, and a specific mental model of how data, code and workflows all come together.</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[http://www.r-bloggers.com/ '''R''' bloggers]</div>
 
−
<div class="content">A digest of new blog-posts on R - from the introductory to the highly advanced. Sent out once every day or two. Really worthwhile subscription.</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[http://blog.revolutionanalytics.com/2017/01/cran-10000.html Package finding strategies]</div>
 
−
<div class="content">(Revolutions Analytics Blog)</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[https://www.datacamp.com/community/tutorials/r-packages-guide Intro to R packages]</div>
 
−
<div class="content">(at DataCamp)</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[https://stackoverflow.blog/2017/10/10/impressive-growth-r/ "The Impressive Growth of R"]</div>
 
−
<div class="content">(Stackoverflow Data Analytics Team Blog)</div>
 
−
</div>
 
−
 
 
−
 
 
−
<div class="resource">
 
−
<div class="name">[http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005871 '''Ten simple rules''' for biologists learning to program]</div>
 
−
<div class="content">Carey and Papin advise novice biologist programmers how to begin. Much of this paper resonates well with our Introduction to R learning units. Good context for a beginning, to get a sense of where we are going with this.</div>
 
−
</div>
 
  
−
</div><!-- END three col block -->
+
{{Vspace}}
  
−
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec in turpis sit amet massa sagittis auctor vitae pharetra lacus. Donec iaculis felis augue, id bibendum neque mattis vel. Aenean porttitor est a aliquam sodales. Donec commodo pulvinar bibendum. Sed leo tellus, ultricies a vehicula vitae, rhoncus ac sem. Maecenas dapibus orci ac sem euismod malesuada. Morbi tempor, libero at imperdiet varius, leo mi tincidunt tortor, sit amet condimentum enim dolor in velit. Pellentesque eu nulla erat. Curabitur nunc arcu, pharetra nec mi ac, tincidunt venenatis quam. Etiam vitae commodo tellus. Ut efficitur gravida massa vitae congue. Quisque scelerisque volutpat velit non iaculis. Proin ullamcorper nisl lacus, maximus elementum erat faucibus vitae. Fusce iaculis quis libero vel fringilla. Morbi efficitur, magna nec convallis malesuada, nulla arcu ornare urna, eu molestie eros ligula quis diam. Nulla facilisi. Fusce bibendum massa in arcu finibus congue. Ut sem felis, scelerisque ut mollis sed, pharetra non magna. Pellentesque aliquet sit amet felis ut condimentum. Suspendisse id est aliquet, pulvinar tellus tristique, egestas eros. Morbi quis mattis urna, id vehicula urna.
+
'''Conclusion and outlook'''
 +
----
  
 +
* Creating layouts, applying styles, adding nodes and edges with Cytoscape seems straightforward and creates evocative images.
 +
* Analyzing and interpreting the network needs more thought. Need to explore ideas and tools for network analysis next - e.g. clustering tools, enrichment tools, motif discovery ...
 +
* Next: write some code to create attribute values for nodes, import the values, and have Cytoscape style the nodes accordingly.
  
−
<div class="two-col"><!-- BEGIN two col block -->
+
<!-- =========================== END sample entry ========================== -->
  
−
===Lorem ipsum===
+
{{Vspace}}
  
−
... dolor sit amet, consectetur adipiscing elit. Donec in turpis sit amet massa sagittis auctor vitae pharetra lacus. Donec iaculis felis augue, id bibendum neque mattis vel. Aenean porttitor est a aliquam sodales. Donec commodo pulvinar bibendum. Sed leo tellus, ultricies a vehicula vitae, rhoncus ac sem. Maecenas dapibus orci ac sem euismod malesuada. Morbi tempor, libero at imperdiet varius, leo mi tincidunt tortor, sit amet condimentum enim dolor in velit. Pellentesque eu nulla erat.
+
----
  
−
===Curabitur nunc===
+
<!-- Footnotes -->
 +
==Notes and References==
 +
<references />
  
−
... arcu, pharetra nec mi ac, tincidunt venenatis quam. Etiam vitae commodo tellus. Ut efficitur gravida massa vitae congue. Quisque scelerisque volutpat velit non iaculis. Proin ullamcorper nisl lacus, maximus elementum erat faucibus vitae. Fusce iaculis quis libero vel fringilla. Morbi efficitur, magna nec convallis malesuada, nulla arcu ornare urna, eu molestie eros ligula quis diam. Nulla facilisi. Fusce bibendum massa in arcu finibus congue. Ut sem felis, scelerisque ut mollis sed, pharetra non magna. Pellentesque aliquet sit amet felis ut condimentum. Suspendisse id est aliquet, pulvinar tellus tristique, egestas eros. Morbi quis mattis urna, id vehicula urna.
+
{{Vspace}}
  
 +
<!-- Category and Footer -->
 +
[[Category:BCH441-2020_Journal]]
  
−
</div><!-- END two col block -->
+
----
  
 +
{{CC-BY}}
  
−
Lorem ipsum dolor sit amet, consectetur adipiscing elit. Donec in turpis sit amet massa sagittis auctor vitae pharetra lacus. Donec iaculis felis augue, id bibendum neque mattis vel. Aenean porttitor est a aliquam sodales. Donec commodo pulvinar bibendum. Sed leo tellus, ultricies a vehicula vitae, rhoncus ac sem. Maecenas dapibus orci ac sem euismod malesuada. Morbi tempor, libero at imperdiet varius, leo mi tincidunt tortor, sit amet condimentum enim dolor in velit. Pellentesque eu nulla erat. Curabitur nunc arcu, pharetra nec mi ac, tincidunt venenatis quam. Etiam vitae commodo tellus. Ut efficitur gravida massa vitae congue. Quisque scelerisque volutpat velit non iaculis. Proin ullamcorper nisl lacus, maximus elementum erat faucibus vitae. Fusce iaculis quis libero vel fringilla. Morbi efficitur, magna nec convallis malesuada, nulla arcu ornare urna, eu molestie eros ligula quis diam. Nulla facilisi. Fusce bibendum massa in arcu finibus congue. Ut sem felis, scelerisque ut mollis sed, pharetra non magna. Pellentesque aliquet sit amet felis ut condimentum. Suspendisse id est aliquet, pulvinar tellus tristique, egestas eros. Morbi quis mattis urna, id vehicula urna.
+
<!-- END -->

Revision as of 07:12, 17 September 2020


Sample Journal


 



 

<my activity>

Objective
text ...

Time estimated: XXX h; taken XXX h;
Date started: 2020-MM-DD; completed: 2020-MM-DD

Progress

Activity 1
Notes ...
Activity 2
Notes ...

Conclusion and outlook

Describe ...


 



(Example Journal Entry) Explore Cytoscape

Objective
Write R code to generate a random network. Explore it with Cytoscape.

Time estimated: 2 h; taken 4 h;
Date started: 2017-09-16; completed: 2017-09-18

Progress

R code for a random network.
Cytoscape can read networks in SIF format. Wrote the following code to generate N random nodes with random interactions and write them to file.

My R code below ... 

N <- 15  # number of nodes
nMin <- 1 # minimum number of edges
nMax <- 5 # maximum number of edges
OUT <- "myRandomSIF.txt"

# Create N random strings from three uppercase characters
# First make more than we need, because some might not be unique ...
nodes <- character(2*N)

set.seed(161803)
for (i in 1:(2*N)) {
  nodes[i] <- paste0(sample(LETTERS, 1),
                     sample(LETTERS, 1),
                     sample(LETTERS, 1))
}
set.seed(NULL)

nodes <- unique(nodes) # throw away duplicates ...
nodes <- nodes[1:N]    # ... and keep only N

# Create SIF output
mySIF <- character()

set.seed(112358)
for (myA in nodes) {  # for each node
  for (i in 1:sample(nMin:nMax, 1)) { # for a random number of interactors ...
    myB <- sample(nodes, 1)           # ... randomly choose interactor ...
                                      # ... create record and apend to mySIF
    mySIF <- c(mySIF, sprintf("%s\tpp\t%s", myA, myB)) # myA, "pp", myB
                                                       # separated by tabs
  }
}
set.seed(NULL)

# write mySIF to file
writeLines(mySIF, OUT)
Install Cytoscape
Straightforward installation of Cytoscape 3.5.1 from http://www.cytoscape.org
Visualize and explore options


 

Conclusion and outlook

  • Creating layouts, applying styles, adding nodes and edges with Cytoscape seems straightforward and creates evocative images.
  • Analyzing and interpreting the network needs more thought. Need to explore ideas and tools for network analysis next - e.g. clustering tools, enrichment tools, motif discovery ...
  • Next: write some code to create attribute values for nodes, import the values, and have Cytoscape style the nodes accordingly.


 

Notes and References


 

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