Changes between Version 1 and Version 2 of doc/net.sf.basedb.meludi.usermanual_start


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Timestamp:
Nov 30, 2016, 12:31:36 PM (4 years ago)
Author:
olle
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  • doc/net.sf.basedb.meludi.usermanual_start

    v1 v2  
    55== 1 Introduction ==
    66
    7 Welcome to MeLuDI, a BASE extension package with registration wizards for melanoma-lung cancer projects.
     7Welcome to MeLuDI, a [http://base.thep.lu.se BASE] extension package with registration wizards for melanoma-lung cancer projects.
    88
    9 === 1.1 Description ===
     9=== 1.1 What's in this manual ===
    1010
    11 MeLuDI 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.
     11This manual is intended to be helpful for the daily user of MeLuDI. Sections marked with an asterisk (`*`) are not absolutely essential to using the software, and can be skipped, if an answer to a specific question is desired. However, the reason for including these sections at all, is that they may add to the total understanding of the context in which MeLuDI works and was developed.
    1212
    13 === 1.2 Background ===
     13=== 1.2 *Background (for history buffs) ===
    1414
    1515==== 1.2.1 BASE ====
     
    1717
    1818==== 1.2.2 Reggie ====
    19 BASE 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 
     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 digital distribution.
    2120
    2221==== 1.2.3 MeLuDI mid-2014 - mid-2016 ====
    2322[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.
    24 It 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.
     23It was named "MeLuDI" after the original project it was developed for, which got its name from "melanoma/lung cancer diagnostics". (When the name "MeLuDI" is used in this document without further specification, the reference is to the software.) 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.
    2524
    2625==== 1.2.4 MeLuDI fall-2016 - ====
    2726During 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.
     27
     28=== 1.3 *Motivation for use ===
     29
     30==== 1.3.1 Why use a database to store LIMS info in? ====
     31
     32The excellent search abilities of a database, especially a relational database, is normally enough to justify its use.
     33
     34==== 1.3.2 Why use BASE? ====
     35
     36If you work with a genomics project, BASE provides a convenient interface to the underlying database:
     37
     38 a. Listings of items like samples, extracts, bioplates, etc. can be easily selected from menus, and filters and sorting rules can be entered in a simple way.
     39 b. BASE is built with a knowledge of the relationship between the different items, e.g. an extract item can be created from the page describing the parent sample/extract, and the created extract will automatically be linked to the parent item, and the new child item will appear on the page for the latter.
     40 c. BASE contains tools to simplify import/export of data in batch-mode, e.g. batch import can be made from definitions in a text file with tabular data in tab-separated columns.
     41 d. Project and user management. BASE allows data to be coupled to a project item, and the system normally only shows items for that project, but items can also be shared to several projects. User administration is also included, where a user can be given different sets of permissions in different projects.
     42 e. Support for two-factor authentication for increased security.
     43 f. Web-based interface. When BASE was first conceived, not all database management systems had web-based interfaces.
     44
     45The decision whether to use BASE or not, often depends on the prevalent digital infra-structure for the laboratory. Much of the work in creating a new BASE installation is related to setting up the server and installing the database, that BASE will use. If a BASE installation already is present in the laboratory, much is simplified. However, the final decision may also depend on other conditions, e.g. requirements to use another LIMS system by regulations or policy decisions.
     46
     47==== 1.3.3 Why use MeLuDI? ====
     48
     49Although genomics data can be entered directly in BASE, if you are working in a project with a workflow similar to that covered by MeLuDI, its use will simplify several things:
     50
     51 a. Creation of multiple extract items from the same parent sample/extract item in BASE requires performing the same operation repeated times. MeLuDI allows all necessary data to be entered in a wizard, after which it creates the new items with needed database links and attached information.
     52 b. MeLuDI provides support for naming conventions for different items in a project, something BASE is ignorant of. Specific prefixes and number of digits in serial numbers may be chosen for items such as samples, item lists, storage boxes, library plates, patient items, and library preparation kits. This is also supported by the system proposing serial numbers in names for new items, as well as storage box positions.
     53 c. MeLuDI uses a suffix system for names of child items inherited from Reggie, where specimens have a dot plus a number added to the case name, DNA extracts have ".d" added to the parent name, FPA aliquots have ".fpa" added to the parent DNA name, etc. This allows the parent heritage items to be identified for an extract directly from the name.
     54 d. Support exists for creating input configuration files with selected sample names for various instruments, as well as importing measurement values from text files generated by the instruments. Files can also be created for label printers.
     55 e. MeLuDI allows creation of dilution protocols, plate layouts, and statistical reports in formats, that are suited both for inspection on a screen and for print-outs.
     56 f. Information related to the same case can be conveniently displayed in a summary page, with links to the individual BASE items, for further inspection in BASE.