| 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 | | |
| | 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 digital distribution. |
| | 27 | |
| | 28 | === 1.3 *Motivation for use === |
| | 29 | |
| | 30 | ==== 1.3.1 Why use a database to store LIMS info in? ==== |
| | 31 | |
| | 32 | The 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 | |
| | 36 | If 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 | |
| | 45 | The 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 | |
| | 49 | Although 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. |
