Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Epic Link:
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Sprint:Sprint 5
Description
Check everything looks the same. They should be identical, but because some files have to be added and maintained by hand, there may be some differences. When you find differences, make note of them here: https://basecamp.com/2734534/projects/7303664/documents/6906502.
Attachments
Activity
*Link to Assignment Document in Basecamp:
https://basecamp.com/2734534/projects/7303664/documents/6906502
October 2014 - Comparing IgbQuickload.org/quickload to BioViz.org/quickload
I have thoroughly compared IGBQuickload.org/quickload to Bioviz.org/quickload and I've noticed several differences. Below are notes on what needs to be changed on Bioviz.org/quickload so that it matches IGBQuickload.org/quickload (However, you may wish to apply these notes to change the IGBQuickload.org site, for example, in areas where the Bioviz.org contained a description or even a "HEADER.html" file but the other site did not).
*Main Page (http://bioviz.org/quickload/):
~Add description for:
~There should not be a "HEADER.html" on the page.
***During my comparisons of the Quickload sites I started noticing a few consistent differences:
1) Below are pages in which the "annots.xml" file had a question mark icon but should have had a document icon:
-http://bioviz.org/quickload/A_lyrata_Apr_2011/
-http://bioviz.org/quickload/A_thaliana_Apr_2008/
-http://bioviz.org/quickload/A_thaliana_Jan_2004/
-http://bioviz.org/quickload/B_distachyon_Aug_2010/
-http://bioviz.org/quickload/C_albicans_SC5314_Nov_2008/
-http://bioviz.org/quickload/C_albicans_WO-1_Jul_2010/
-http://bioviz.org/quickload/C_papaya_Aug_2010/
-http://bioviz.org/quickload/C_reinhardtii_Nov_2010/
-http://bioviz.org/quickload/E_coli_K12-MG1655_Jan_2012/
-http://bioviz.org/quickload/F_vesca_Sep_2011/
-http://bioviz.org/quickload/G_max_Aug_2010/
-http://bioviz.org/quickload/M_truncatula_Mar_2009/
-http://bioviz.org/quickload/O_sativa_japonica_Jun_2009/
-http://bioviz.org/quickload/P_patens_Jan_2008/
-http://bioviz.org/quickload/P_persica_Apr_2010/
-http://bioviz.org/quickload/P_trichocarpa_Jan_2010/
-http://bioviz.org/quickload/R_communis_May_2008/
-http://bioviz.org/quickload/S_bicolor_Jan_2009/
-http://bioviz.org/quickload/S_lycopersicum_Feb_2014/
-http://bioviz.org/quickload/S_pombe_May_2012/
-http://bioviz.org/quickload/T_castaneum_Mar_2008/
-http://bioviz.org/quickload/T_kodakaraensis_KOD1_May_2004/
-http://bioviz.org/quickload/V_carteri_Jul_2010/
-http://bioviz.org/quickload/V_vinifera_Mar_2010/
-http://bioviz.org/quickload/Z_mays_B73_Mar_2010/
2) Below are pages in which the "HEADER.html" file should be removed (since the IGBQuickload/quickload pages do not contain it, but maybe you would rather add this file to IGBQuickload.org).
-http://bioviz.org/quickload/A_thaliana_Jun_2009/Affymetrix/
-http://bioviz.org/quickload/A_thaliana_Jun_2009/cold_stress/
-http://bioviz.org/quickload/A_thaliana_Jun_2009/EST/
-http://bioviz.org/quickload/A_thaliana_Jun_2009/LFYChIPSeq/
-http://bioviz.org/quickload/A_thaliana_Jun_2009/mRNA/
*Points 1) and 2) from above were seen together in these pages:
-http://bioviz.org/quickload/A_gambiae_Feb_2003/
-http://bioviz.org/quickload/A_melanoleuca_Dec_2009/
-http://bioviz.org/quickload/A_mellifera_Jan_2005/
-http://bioviz.org/quickload/A_thaliana_Jun_2009/
-http://bioviz.org/quickload/B_taurus_Oct_2011/
-http://bioviz.org/quickload/C_elegans_May_2008/
-http://bioviz.org/quickload/C_elegans_Oct_2010/
-http://bioviz.org/quickload/C_porcellus_Feb_2008/
-http://bioviz.org/quickload/D_discoideum_Ax4_May_2009/
-http://bioviz.org/quickload/D_melanogaster_Apr_2006/
-http://bioviz.org/quickload/D_rerio_Jul_2010/
-http://bioviz.org/quickload/E_caballus_Sep_2007/
-http://bioviz.org/quickload/F_catus_Dec_2008/
-http://bioviz.org/quickload/F_catus_Sep_2011/
-http://bioviz.org/quickload/G_gallus_Nov_2011/
-All versions of the Human Genome
-http://bioviz.org/quickload/L_africana_Jul_2009/
-http://bioviz.org/quickload/M_domestica_Oct_2006/
-http://bioviz.org/quickload/M_musculus_Dec_2011/
-http://bioviz.org/quickload/M_musculus_Jul_2007/
-http://bioviz.org/quickload/N_vectensis_Jun_2007/
-http://bioviz.org/quickload/O_aries_Feb_2010/
-http://bioviz.org/quickload/O_sativa_japonica_Oct_2011/
-http://bioviz.org/quickload/P_trichocarpa_Aug_2012/
-http://bioviz.org/quickload/P_troglodytes_Oct_2010/
-http://bioviz.org/quickload/R_norvegicus_Mar_2012/
-http://bioviz.org/quickload/S_cerevisiae_Apr_2011/
-http://bioviz.org/quickload/S_lycopersicum_May_2012/
-http://bioviz.org/quickload/T_parvula_May_2012/
-http://bioviz.org/quickload/T_rubripes_Oct_2011/
-http://bioviz.org/quickload/X_tropicalis_Nov_2009/
3) Below are pages in which the "README.html" should be removed (since the IGBQuickload/quickload pages do not contain it, but maybe you would rather add this file to IGBQuickload.org).
-http://bioviz.org/quickload/T_castaneum_Mar_2008/ (there is also a "README.txt" file not present on the other site)
-http://bioviz.org/quickload/A_thaliana_Jun_2009/LFYChIPSeq/
-http://bioviz.org/quickload/C_albicans_SC5314_Nov_2008/
-http://bioviz.org/quickload/C_albicans_WO-1_Jul_2010/
4) For these pages, descriptions must be added/removed/changed (These instructions will ensure that Bioviz.org matches the current IGBQuickload.org, but maybe you would rather have it so that IGBQuickload.org macthes the current Bioviz.org):
-http://bioviz.org/quickload/D_discoideum_Ax4_May_2009/ ="D_discoideum_Ax4_May_2009.fa.gz" description should read "Slime mold" instead of "Sequence data in fasta format".
-All versions of the human genome = "cytoBand.cyt" should say "Cytobands file" in the description.
-http://bioviz.org/quickload/P_patens_Jan_2008/SRP019809_processed/ = "sm.bam" and "mm.bam" files should not have "single-mapping reads only/multi-mapping reads only" in description.
-http://bioviz.org/quickload/S_bicolor_Jan_2009/SRP007361/ = "sm.bam" and "mm.bam" files should not have "single-mapping reads only/multi-mapping reads only" in description.
-http://bioviz.org/quickload/T_kodakaraensis_KOD1_May_2004/ = description of T_kodakaraensis_KOD1_May_2004.fa.gz should read "Thermococcus kodakaraensis" instead of "Sequence data in fasta format".
-http://bioviz.org/quickload/Z_mays_B73_Mar_2010/SRP006463/ = "sm.bam" and "mm.bam" files should not have "single-mapping reads only/multi-mapping reads only" in description.
-http://bioviz.org/quickload/A_thaliana_Jan_2004/ = Chr#.bnib files should not have "Sequence data in BNIB (IGB specific) format" in description.
-http://bioviz.org/quickload/A_thaliana_Jun_2009/cold_stress/ = "sm.bam" and "mm.bam" files should not have "single-mapping reads only/multi-mapping reads only" in description.
-http://bioviz.org/quickload/A_thaliana_Jun_2009/fastq/ = Descriptions of "BA1_2.fastq.gz" reads "Sequence data in fastA format" rather than "Sequence data in fastQ format".
-http://bioviz.org/quickload/A_thaliana_Jun_2009/LFYAtTile1R/ = "ma.bar" files should not have "Binary array data" in description.
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5) Change the Titles of these pages:
-http://bioviz.org/quickload/C_albicans_SC5314_Nov_2008/ = Title should be "Index of /C_albicans_SC5314_Nov_2008" instead.
-http://bioviz.org/quickload/C_albicans_WO-1_Jul_2010/ = Title should be "Index of /C_albicans_WO-1_Jul_2010" instead.
6)Other issues that were not seen consistently:
-http://bioviz.org/quickload/A_thaliana_Jun_2009/ = "LFY-ChIP-Chip.xml" & "LFY-ChIP-Seq.xml" have a question mark icon but they should have document icons.
-http://bioviz.org/quickload/C_albicans_SC5314_Nov_2008/ = "C_albicans_SC5314_version_A21-s02-m01-r11_features.gff" has a question mark icon but it should have a document icon.
-There is no header for these pages:
-http://bioviz.org/quickload/A_thaliana_Jun_2009/LFYAtTile1R/
-http://bioviz.org/quickload/A_thaliana_Jun_2009/LFYChIPSeq/
If changes are made according to these notes then IGBQuickload.org/quickload should be identical to Bioviz.org/quickload except for the footer [Apache/2.2.15 (Red Hat) Server at igbquickload.org Port 80] that IGBQuickload.org/quickload contains while Bioviz.org/quickload does not. Please let me know if you have any questions.
-Mason