QLanners Week 9

Electronic Journal

GRNsight Client Side Testing Document: Edge Weights + Gray Threshold

• Test 1
  • Passed
• Test 2
  • Passed
• Test 3
  • Passed
• Test 4
  • Passed
• Test 5
  • Passed
• Test 6
  • Passed
• Test 7
  • Passed
• Test 8
  • Passed
• Test 9
  • Passed
• Test 10
  • Passed
• Test 11
  • Passed
• Test 12
  • Passed
• Test 13
  • Passed
• Test 14
  • Passed
• Test 15
  • Passed
• Test 16
  • Passed
• Test 17
  • Passed
• Test 18
  • Passed

• Other Notes:
  • Every time you change the "Gray Edge Threshold" the Zoom level of the viewport resets itself. This makes it difficult to use the gray edge threshold, as you lose track of the genes you were paying attention to if you were zoomed in or out.
  • The first time I tried to load SIF and GRAPHML files on 10/24, the program would allow me to select my file, but nothing would load. However, when I tried again on 10/26 both file types were loaded normally. Not sure if this was an issue with my local computer or the application itself. This error took place on both Safari and Chrome the first time I tried but worked on both browsers the second try.

Web Service API Exploration

• Goal: To take a gene name and find a path to its full data profile
• Assigned database: NCBI
• Dondi References:
  • Relevant documentation:
    • https://www.ncbi.nlm.nih.gov/gene
    • https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch
    • https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Searching_a_Database
    • https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Document_Summaries
    • https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Downloading_Full_Records
  • Technical information:
    • Your URLs will include ampersands (&), which will need special handling with curl: in these cases, enclose the URL in apostrophes (e.g., curl -L 'http://www.uniport.org?query=this&type=that')
    • Your URLs will also include brackets ([ ]), which will need special handling with curl: in these cases, make sure to add the -g switch (i.e., curl -g …)
    • Your URLs may include spaces; typically, we replace those with + (plus) symbols
  • Miscellaneous information:
    • NCBI consists of multiple databases; we care about the gene database
    • NCBI abbreviates the gene name/symbol field as sym
    • NCBI stores organisms by their full name, in our case Saccharomyces cerevisiae (note the space)
• Solution: