diff --git a/DESCRIPTION b/DESCRIPTION index 43bb0fe..9687e75 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: MsBackendSql Title: SQL-based Mass Spectrometry Data Backend -Version: 1.3.0 +Version: 1.3.1 Authors@R: c(person(given = "Johannes", family = "Rainer", email = "Johannes.Rainer@eurac.edu", diff --git a/NEWS.md b/NEWS.md index 1325597..c164ef5 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +# MsBackendSql 1.3 + +## Changes in 1.3.1 + +- Add description on the use/advantages of different SQL database systems to the + vignette. + # MsBackendSql 1.1 ## Changes in 1.1.5 diff --git a/vignettes/MsBackendSql.Rmd b/vignettes/MsBackendSql.Rmd index 94236c3..d9a06bf 100644 --- a/vignettes/MsBackendSql.Rmd +++ b/vignettes/MsBackendSql.Rmd @@ -363,6 +363,29 @@ The `MsBackendSql` outperforms the `MsBackendMzR` while, not unexpectedly, the `MsBackendMemory` provides fasted access. +## Considerations for database systems/servers + +The backends from the *MsBackendSql* package use standard SQL calls to retrieve +MS data from the database and hence any SQL database system (for which an R +package is available) is supported. SQLite-based databases would represent the +easiest and most user friendly solution since no database server administration +and user management is required. Indeed, performance of SQLite is very high, +even for very large data sets. Server-based databases on the other hand have the +advantage to enable a centralized storage and control of MS data (inclusive user +management etc). Also, such server systems would also allow data set or +server-specific configurations to improve performance. + +A comparison between a SQLite-based with a MariaDB-based *MsBackendSql* database +for a large data set comprising over 8,000 samples and over 15,000,000 spectra +is available +[here](https://github.com/rformassspectrometry/MsBackendSql/issues/15). In +brief, performance to extract data was comparable and for individual spectra +variables even faster for the SQLite database. Only when more complex SQL +queries were involved (combining several primary keys or data fields) the more +advanced MariaDB database outperformed SQLite. + + + # Other properties of the `MsBackendSql` The `MsBackendSql` backend does not support parallel processing since the