Changes between Version 4 and Version 5 of Ticket #690, comment 2


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Timestamp:
Nov 14, 2014, 10:56:14 AM (10 years ago)
Author:
olle

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  • Ticket #690, comment 2

    v4 v5  
    44 * The new BASE plug-in registration package ''!MeLuDi'' for melanoma/lung cancer projects, will be based on Reggie, where possible, but will be a stand-alone package. The advantages of using Reggie as model are numerous:[[BR]][[BR]]a. Faster development. Many operations are fully or nearly identical for the two projects, and using the Reggie code base will reduce development time.[[BR]]b. More stable code. Reggie has already been through several cycles of development iterations, where found bugs have been fixed, and new code has been written with previous experiences in mind.[[BR]]c. More streamlined code. The development iterations have also led to more streamlined code design.[[BR]]d. A consistent user interface. Having a consistent user interface is an advantage in itself. Basing !MeLuDi on Reggie will have a two-fold advantage, since lab personnel used to Reggie, will need less time to adapt to !MeLuDi.[[BR]][[BR]]Using Reggie code as inspiration, will hopefully transfer a lot of the benefits listed above to !MeLuDi. Unfortunately, the differences in lab procedure are too big to allow the latter as being developed as a branch of the Reggie code. The source code will therefore be entered in the subversion source code revision system as an independent package.
    55
    6 Differences between lab procedures and data management in !MeLuDi and Reggie:
     6Differences between lab procedures and data management in Reggie and !MeLuDi (list not complete):
    77
    88|| '''Item''' || '''Reggie''' || '''!MeLuDi''' ||
    … …  
    1010|| Sample types || `Specimen`, `NoSpecimen`, `Blood`, `Follow-up blood` || `Primary`, `MetastasisDistant`, `DNA`, `RNA` ||
    1111|| Normal sample distribution || Tissue specimen || FFPE (Formalin-Fixed, Paraffin-Embedded) tissue ||
     12|| Site || Used (indicated by first 2 figures in case name) || Used, but may be unknown. Stored as annotation. ||
     13|| Consent || Used || Not used (patients may have been asked for consent, but this is not tracked in this database) ||
    1214|| Laterality || Used || Not used ||
     15|| RNALaterDateTime || Used || Not used ||
     16|| PL-number || Not used || Number similar to PAD (Patho-Anatomical Diagnosis) number, written on label on referral form, and always starting with letters "`PL`".
     17|| Mutation analysis || Not used || Used. Selection of options, initially `KRAS/NRAS` (exon 2-4), `BRAF` (codon 600), `EGFR` (exon 18-21).
     18|| Histology-related items || Used || Not used ||
     19|| Lysates || Used || Not used ||
     20|| !FlowThrough || Used || Not used ||