Projects and Workspaces

Introduction

This tutorial was prepared using Genome Workbench version 2.7.0

All the illustrations in this tutorial are taken from our Microsoft Windows 7 product release. Unix/Linux users, Mac users, and users of the other MS Windows versions might see minor variations in default settings, column order, window size, etc.

Genome Workbench organizes data around the concept of "Project". A "Project" is a named container, grouping information related to a certain topic of study. Projects can contain references to known molecules, sequence information, annotations, alignments, phylogenetic trees, etc. Projects can be named, saved and later reopened. Projects can organize data into folders.

"Projects" can also be assigned to "Workspaces". A single "Workspace" contains one or more "Projects". It also can be saved and restored. Projects contained within a Workspace are opened automatically with the Workspace.

Workspace and project

This tutorial will take you through the steps necessary to understand how the Project and Workspace entities work together in Genome Workbench.

Step 1. Download Experiment File

Please download the GFF3 experiment file.

Step 2. Add molecules to project

Open molecules:

CM001064.1 CM001065.1 CM001066.1 CM001067.1 CM001068.1 CM001069.1 CM001070.1 CM001071.1 CM001072.1 CM001073.1 CM001074.1 CM001075.1

Open Molecules Dialog

The result should look similar to this:

Molecules Loaded into the project

Step 3. Import GFF file

Open the GFF file with gene models.

Import the GFF file

Choose Create a New Project for the imported data.

Choose to create a New Project

Step 4. Remap local ids to accesions

The GFF3 file is formulated to use local ids, instead of accessions - use remapping information to import with accession ids.

SL2.40ch01 CM001064.1 SL2.40ch02 CM001065.1 SL2.40ch03 CM001066.1 SL2.40ch04 CM001067.1 SL2.40ch05 CM001068.1 SL2.40ch06 CM001069.1 SL2.40ch07 CM001070.1 SL2.40ch08 CM001071.1 SL2.40ch09 CM001072.1 SL2.40ch10 CM001073.1 SL2.40ch11 CM001074.1 SL2.40ch12 CM001075.1

Remap GFF ids

Step 5. Open Graphical View

Now your workspace contains two projects. If you open a molecule from one project with Graphical View you will not see your annotations from the other project.

Two projects and Graphical Sequence View

Step 6. Move annotations and molecules into one project

Fix this by moving annotations and molecules into a single project. When it is done the Graphical View (and all other views) will show the new annotation track.

One projects and Graphical Sequence View

Broadcast settings

When working with multiple projects it is important that you turn on event broadcasting between projects using the Tools/Broadcast options menu.

One projects and Graphical Sequence View

Potential errors

Genome Workbench can potentially construct an "incomplete" project - for example you can go online and align two sequences using BLAST (or any other alignment tool), then import alignments into Project. Such alignments would refer to some local sequences. Attempt to open the alignment in any Alignment View (like Multiple Alignment View) will result in errors like "Invalid bioseq handle. Seq id lcl|XXXXX". It means that alignment refers to unknown sequences (not loaded into Project). If you use your FASTA file to load it into project - it becomes resolvable. Same rule applies to any annotation loaded without sequence.

Alignment spanview error

Conclusion

Genome Workbench allows you to better structure your work with Projects and Workspaces. It is important to remember that IDs are resolved within the scope of a single Project. Related sequences and annotations should therefore be loaded into the same Project. This applies both to molecules with NCBI accessions and to local data (imported from FASTA as well as annotation files like GFF).

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Last updated: 2017-11-04T03:25:26Z