Mason Meyer (Inactive) added a comment - 17/Oct/14 8:22 AM *Link to Assignment Document in Basecamp: https://basecamp.com/2734534/projects/7303664/documents/6906502

Mason Meyer (Inactive) added a comment - 17/Oct/14 8:21 AM - edited 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: H_sapiens_Dec_2013/ = Homo sapiens hg38 (Genome Reference Consortium GRCh38) H_sapiens_Mar_2006/ = Homo sapiens hg18 (Genome Reference Consortium GRCh36) H_sapiens_May_2004/ = Homo sapiens hg17 (Genome Reference Consortium GRCh35) S_lycopersicum_Feb_2014/ = Solanum lycopersicum (Feb 2014) tomato (SL2.50) ~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. - 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