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= MeLuDI Software Information =

== 1 Introduction ==
=== 1.1 Description ===
MeLuDI is an ''extension package'' to BASE with registration wizards for melanoma-lung cancer projects, in analogy with the package "Reggie" for the SCAN-B breast cancer project. It is named "MeLuDI" after "melanoma/lung cancer diagnostics". This page gives some background information on the software, and is not intended as a user manual. Instead, some behind-the-scene information is given, e.g. what item properties are used to track what steps in the lab processing pipeline an item has passed, which can be useful, if you want to check items for a specific step directly in BASE, or re-do a step, if an error occurred.

=== 1.2 Links ===

 - BASE (!BioArray Software Environment) is a comprehensive free web-based database LIMS solution for tracking of information and data generated in sequencing and microarray experiments from sample to analysis. BASE is released under the ​[http://www.gnu.org/licenses/gpl.html GNU General Public License version 3]. It can be accessed at http://base.thep.lu.se/.
 - Reggie is an ''extension package'' to BASE that makes it easier to register biosources and samples. It can be accessed at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie.
 - MeLuDI can be accessed at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.meludi.

=== 1.3 MeLuDI: The project, and MeLuDI: The software ===
"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.
As 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.

=== 1.4 Note on BASE annotations ===
BASE 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 was 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.

=== 1.5 Pipeline management ===
MeLuDI, 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 items 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. One case where you might be interested in the details of how MeLuDI keeps track of what steps an item has passed, is when you want to undo a step in the BASE GUI by deleting child items created in the last step. Sometimes this is not enough to allow you to redo the last step in MeLuDI, since the needed items do not appear in selection menus, if the software still considers them to have passed the step in question.

==== 1.5.1 Wizard "Lab tracking protocol for FFPE extraction": Extract source items added to start list ====
Extract source items (specimens or input extracts) added to a start list have their original quantity changed from `null` to 0.0. This will stop them from appearing in the extract source item selection menu, when the wizard is run again.
==== 1.5.2 Wizard "DNA/RNA registration/quantification": Processing a start list
A start list is regarded as processed, when quantification data for its extracts have been entered. This is indicated by setting value of Boolean item list annotation `Annotationtype.SAMPLE_PREP_LIST_IS_PROCESSED` to `true`.
==== 1.5.3 Wizard "Create new start DNA plate" Step 1: Processed start list to select DNA extracts from
Only processed start lists with at least one DNA extract without an FPA child extract on a library plate will appear in the start list selection menu.
==== 1.5.4 Wizard "Create new start DNA plate" Step 2: DNA extracts on selected processed start lists
Only DNA extracts without an FPA child extract on a library plate will appear in the DNA extract selection menu.