Changes between Initial Version and Version 1 of doc/net.sf.basedb.meludi.usermanual_start


Ignore:
Timestamp:
Nov 29, 2016, 4:53:54 PM (4 years ago)
Author:
olle
Comment:

Added initial information

Legend:

Unmodified
Added
Removed
Modified
  • doc/net.sf.basedb.meludi.usermanual_start

    v1 v1  
     1[[PageOutline]]
     2
     3= MeLuDI 1.5.0 User Manual =
     4
     5== 1 Introduction ==
     6
     7Welcome to MeLuDI, a BASE extension package with registration wizards for melanoma-lung cancer projects.
     8
     9=== 1.1 Description ===
     10
     11MeLuDI is an ''extension package'' to [http://base.thep.lu.se BASE] with registration wizards for melanoma-lung cancer projects, in analogy with the package "Reggie" for the [http://scan.bmc.lu.se/index.php/Main_Page SCAN-B Primary] breast cancer project.
     12
     13=== 1.2 Background ===
     14
     15==== 1.2.1 BASE ====
     16[http://base.thep.lu.se BASE] was developed as a free web-based database LIMS solution for tracking of information and data generated in sequencing and microarray experiments from sample to analysis.
     17
     18==== 1.2.2 Reggie ====
     19BASE extension package [http://baseplugins.thep.lu.se/wiki/net.sf.basedb.reggie Reggie] was developed as an interface to BASE, tailored to the laboratory workflow for the [http://scan.bmc.lu.se/index.php/Main_Page SCAN-B] breast cancer project (more accurately, to the part known as SCAN-B Primary). Reggie both simplifies entry of LIMS data into BASE, as well as inspection of the data and production of documents such as dilution protocols and results reports. At the time of writing, Reggie provides help with management of the complete pipeline from incoming samples, through extraction, library preparation, pooling for sequencing, secondary analysis of the NGS sequencing output, report generation and distribution.
     20
     21
     22==== 1.2.3 MeLuDI mid-2014 - mid-2016 ====
     23[http://baseplugins.thep.lu.se/wiki/net.sf.basedb.meludi MeLuDI] was later developed as another BASE extension, based on Reggie, but intended for melanoma-lung cancer projects.
     24It was named "MeLuDI" after the original project it was developed for, which got its name from "melanoma/lung cancer diagnostics". MeLuDI was developed continuously until version 1.4.3, when the original MeLuDI project was terminated. The software then covered a workflow from sample registration to library preparation.
     25
     26==== 1.2.4 MeLuDI fall-2016 - ====
     27During fall 2016, a number of research projects at Lund University involved lab work using a workflow very close to the one used for the original MeLuDI project, so it was decided that a modified version of the MeLuDI software was to be used to track samples. MeLuDI was updated to support use in several BASE projects, allowing different items to have project-specific prefixes and number of digits in names, as well as project-specific default values for a number of items. Created documents like dilution protocols and statistics reports were updated to include the name of the active project. Together with other updates intended to support more flexibility in the workflow, the updated software was released as MeLuDI v1.5.0.