Changes between Version 5 and Version 6 of net.sf.basedb.meludi.background_software_info

Dec 1, 2015, 7:59:02 AM (9 years ago)

Starting section 1.5 on pipeline management


  • net.sf.basedb.meludi.background_software_info

    v5 v6  
    1313 - MeLuDI can be accessed at
    15 === 1.3 MeLuDI, the project, and MeLuDI, the software ===
     15=== 1.3 MeLuDI: The project, and MeLuDI: The software ===
    1616"MeLuDI" (short for "melanoma/lung cancer diagnostics") is the name of a project at the Department of Oncology, Clinical Sciences, Lund University. It produces clinical genomics data from samples from patients having specific types of cancer, but also aims to support cancer research. Originally, the focus was on melanoma and lung cancer, but later on, more cancer types were supported.
    1717As part of the LIMS procedure, it was decided to store sample data in a database managed by BASE, and which normally was accessed through a BASE extension, named "MeLuDI" after the project. The software does not necessarily cover all aspects of the project, it was named after. However, when the name "MeLuDI" is used in this document without further specification, the reference is to the software.
    1919=== 1.4 Note on BASE annotations ===
    2020BASE was developed to be a web-based interface to a database with bio assay data. In order to simplify adapting the software/database to specific data storage needs, a system of annotation types were developed, making it easy to add storage of new variable data to an "annotatable" item. An annotation type is of a specific data type, e.g. integer, float, string; and is defined for a specific type of item, e.g. samples, extracts, bioplates, item lists, etc.
     22=== 1.5 Pipeline management ===
     23MeLuDI, like Reggie, is intended to simplify keeping track on what items are of interest in each step of the processing pipeline, e.g. by only including those item in selection menus for a particular step. In some cases, this is simple, since child items are created at registration in several steps, and will then be input items in the next step.