Chapter 4. Overview of user documentation

Table of Contents

4.1. Working environment
4.2. Start working with BASE
4.2.1. Administrative tasks
4.2.2. User tasks

The 'User documentation' part is quite extensive and covers everything from how to Log in on a BASE server and find your way through the program, to working with experiments and doing some useful analysis. The intention with this chapter is to give an overview of the following chapters so it will be easier for you to know where to look for certain information in case you don't want to read the whole part from the beginning to the end.

4.1. Working environment

Before you start working with any big experiment or project in BASE it could be a good idea to get to know the environment and perhaps personalize some behavior and appearance of the program. When this is done your daily work in BASE will be much easier and you will feel more comfortable working with the program.

Most of the things that have to do with the working environment are gathered in one chapter, where the first subsection, Section 5.1, “Introduction” , gives a good guidance how to start using BASE including a general explanation how to navigate your way through the program.

The second subsection, Section 5.2, “Configuring your account” , describes how to personalize BASE with contact information, preferences and changing password. The preferences are for instance some appearance like date format, text size or the look of the toolbar buttons.

The last two subsections, Section 5.3, “Working with items” and Section 5.4, “Listing items” , in the web client chapter explains how to work with BASE. No matter what you are going to do the user interface contains a lot of common functions that works the same everywhere. For example, how to list and search for items, how to create new items and modify and delete existing items. Subsequent chapters with detailed information about each type of item will usually not include descriptions of the common functionality.

4.2. Start working with BASE

There are some working principles that need to be understood by all users in BASE. These concern the permission system and how to get the workflow to move on without any disturbance caused by insufficient permissions. The key is to work in projects, which is covered in detail in Chapter 6, Projects and the permission system .

Understanding the permission system and how to work in projects will not only make it more simple for you to work in BASE but also for your co-workers who want access to your data.

The next thing to do is to add some relevant data to work with. Most of the different items can be created manually from the web client, but some items and data must be imported from files. Before importing a file, it has to be uploaded on the BASE-server's file system. Chapter 7, File management gives you information about the server's file system and how to upload the files.

Chapter 19, Import of data explains how the import is done and Chapter 20, Export of data covers how data later on can be exported from the database back into files, often simple text files or xml files.

Each different item has it's own section in this part of the documentation, where more specific information and also some screen shots can be found. Go back to the table of contents for this part and look up the item you want to know more about.

4.2.1. Administrative tasks

Most of the tasks in this section require more privileges than the normal user credentials. As always, there are many ways to do things so steps presented here is the path to get going with BASE as fast as possible without creating havoc in future use of the BASE server.

  1. Log in as root using the password you set during BASE initialization. Create an account and give it the administrator-role. Switch user to the new admin account and use this for all future administrative tasks.

    [Note] Note

    The root-account should only be used to create the first administrator account and nothing else.

  2. First thing to do, when logged in as administrator, is to create other user-accounts and give them appropriate roles, most of them should be assigned to the User-role.

    Information related to user-accounts can be found at Chapter 23, Account administration.

  3. Next step for you as an administrator is to import reporter-map and corresponding reporters to BASE. For import of Genepix data you can use the Reporter importer plug-in and Reporter map importer plug-in that come with BASE. Go to Array LIMSArray designs or ViewReporters respectively and start the import from there. You can read more about data-import in Chapter 19, Import of data

4.2.2. User tasks

A normal user is not allowed to add array design, reporter information, and a lot of other information to BASE. The reason for this is that a lot of information should only exist as one copy in the database. For example, reporters should only exist in one copy because everyone uses the same reporters. There is no need to store several copies of the same array design.

A user will normally upload experimental data to BASE for import into the database. To be able to import the data, the array design which is used, must be available in BASE at import time. If the array design is not available, a user with the proper credential must add the array design to BASE.

  1. The first thing for an user to do is creating a project to work in and set this as the active project. This should be done before any other items are created. Section 6.2, “Projects” tell you more about how working in projects can help you and your co-workers.

  2. Next step is to create raw bioassays and up-load raw data to BASE. This is done in the raw bioassay section. (ViewRaw bioassays) . For more information see Section 18.2, “Raw bioassays”.

  3. Now when there are data to work with, you can create your first experiment. You reach the experiment section through the menu ViewExperiments. Further reading in Section 18.3, “Experiments”.

    1. The analysis often starts with the creation of a root bioassay set. Open the recently created experiment and go to the Bioassay sets tab. Click on the New root bioassay set button to start the creation.

    2. With a root bioassay set you can now continue your analysis with different kinds of analysis plug-in. To the right of the each listed bioassay set is a set of icons for the actions that can be performed. Section 18.4, “Analysing data within BASE” goes to the bottom of analysis in BASE.

This concludes the short step-by-step get going text. Far from all functionality in BASE has been covered here. E.g. nothing about LIMS or biomaterials have been mentioned. But you should now at least be familiar with getting to that point when it is possible to do some analysis.