Program
MolQuest integrates various programs for molecular biology data processing. Programs are distributed by their developers in packages. Packages are installed by the main menu command Tools -> Install Package. All available programs are displayed in Programs Sheet of the Toolbox Tab.

Task
In MolQuest, a task is a command to run a program using certain values of its parameters (properties). Same program with two different sets of values of its parameters is considered to represent two different tasks. Current status of a task (being processed, finished, ready) is displayed in Project tab.

Project
Project is the key element and executable unit of MolQuest workflow, consisting of an ordered set of tasks, defined by user. For each new project, MolQuest creates a separate folder. That folder contains subfolders corresponding to each of a project's task, where those tasks' outputs are written and can be accessed by user. A list of a project's tasks is shown in Project tab and Pipeline Tab . While executing a project, only tasks with status Enabled are executed (see Task Status.

Pipeline
An output of a task can be as an input for another task, which creates a sequential order of tasks, called pipeline. The Pipeline tab displays all links between tasks in a pipeline. Predefined pipelines from packages are shown in Pipelines Sheet of Toolbox Tab.

View
Quite often, users run the same program with varied values of program's parameters (properties). Each set Program + Properties can be specified as a separate task: for instance, program P with several different sets of parameters can be defined as several separate tasks, T1, T2 etc. In many cases, however, an alternative approach, which uses MolQuest's concept called View, is more convenient. View is a set of parameters values within a task, so that instead of separate tasks as above we get a set of separate views, V1, V2 etc. Each task has at least one view, Current View, which is used when task is executed. Each of existing views within a task can be set as Current View, which is done when user wants to run a task with a different set of values of program's parameters.

User can not only set parameters to different values, but also hide non-essential parameters from being shown Properties tab. For instance, user can take view V1 and hide all non-essential parameters, creating view V2 - identical in all respects except visual representation of parameter values. This is useful in case of multi-parameter tasks, when only few parameters are varied, while the majority remain the same and are hidden from view in order not to distract user.

Converter
In most cases of pipeline-like queues of tasks, an output of one task, supposed to be used as an input of another task, has format that is incompatible with "downstream" task. To convert an output to format suitable for another program, special auxilliary programs, called converters, are used. In many cases, MolQuest can automatically add an appropriate converter to a pipeline. As most programs, converters are distributed in packages. The Converters Sheet in the Toolbox Tab shows all available converters.