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General Questions

What is Genome Workbench?

Genome Workbench is an integrated application for viewing and analyzing sequences. Genome Workbench can be used to browse data in GenBank and combine this data with your own private data.

Where can I get Genome Workbench?

The current release of Genome Workbench is available by FTP at ftp://ftp.ncbi.nlm.nih.gov/toolbox/gbench/

What platforms does Genome Workbench run on?

Genome Workbench runs natively on Windows 2000/XPVista, Linux, MacOS X (10.4) and various flavors of Unix. We provide binary snapshots of the application for Windows and MacOS X; the source snapshot can be used on any platform.

Are there any mailing lists for Genome Workbench?

Yes - there are several. Some useful e-mail addresses to know:
  • gbench@ncbi.nlm.nih.gov. This is a public list for discussion of Genome Workbench. Any member of the public may post to this list, with moderation; in addition, membership is open.
  • gbench-announce@ncbi.nlm.nih.gov. This is a public list for all Genome Workbench announcements. Any member of the public may belong to this list; posting to this list is limited to approved announcements from NCBI.
  • gbench-bugs@ncbi.nlm.nih.gov. This is an e-mail alias for reporting bugs with Genome Workbench. This alias is the recipient of all feedback reports supplied by Genome Workbench. Membership is limited to the developers of Genome Workbench; however, anyone can post to this list.
  • cpp-gui@ncbi.nlm.nih.gov. This is a list for discussion of Genome Workbench development and general GUI development using the NCBI C++ ToolKit.

Help! I want to do something, but Genome Workbench can't do it! What can I do?

Post a message to the main mailing list, gbench@ncbi.nlm.nih.gov. The list is read by many knowledgeable users at NCBI, as well as application developers. Chances are, we can help find a solution.

Genome Workbench Installation

I've installed Genome Workbench, but it won't run (or takes a really long time to start). What is going on?

The most common problem here is that you are running Genome Workbench behind a restrictive firewall that prevents outbound connections. The possible solutions are:
  • Ask your network administrators to permit outbound connections. This is the most common cause of problems.
  • Configure Genome Workbench to understand your firewall settings. This configuration can be done from within Genome Workbench by following the steps below:
    • Choose the menu item Tools -> Configure Network Connection.
    • There are two drop-down menus in the section entitled NCBI Connection Settings. Please choose the options Connect via NCBI Dispatcher in the first drop-down and Reuse connections to NCBI services if possible in the second.
    • If you have an institution-wide web proxy, please enter the settings into the section entitled HTTP Proxy Settings.
    • If you experience extreme slow-downs with connections, please try changing the second drop-down back to Reuse connections. This may not work behind a firewall, dependening on your firewall's settings.
  • The configuration steps above establish some defaults in a configuration file that you can edit manually if you need to. If you have completed the steps above, you do not need to make any of the changes below; the changes below are merely provided for debugging purposes. An easy place to start is this file, which contains a set of settings that are common enough that most firewall users should be able to work with. This file should be renamed and placed in your Genome Workbench user-specific directory:
    • Windows: C:\Documents and Settings\<login name>\Application Data\GenomeWorkbench\gbench.ini
    • Unix/MacOS X: $HOME/.gbench/gbench.ini
    If you experience any problems, particularly with speed, please remove the line that says 'STATELESS=TRUE' and try again. If you are having trouble with the link above, the file contains the following: 
    [CONN]
FIREWALL = TRUE
STATELESS = FALSE
  • Configure Genome Workbench to understand your HTTP proxy. If you use a corporate HTTP proxy, you may need to adjust Genome Workbench to respect the proxy settings. A sample configuration file is below; this belongs in the same place as the example above: 
    [CONN]
FIREWALL = TRUE
STATELESS = FALSE
HTTP_PROXY_HOST = 10.0.100.1
HTTP_PROXY_PORT = 3128
TIMEOUT=60
  • The firewall settings are available from inside Genome Workbench by using the menu command Tools -> Configure Network Connection.

Genome Workbench Interface

What is a Project? What is a Workspace?

In short: Projects Hold Data. Workspaces Hold Projects. It is best to combine data that go together inside projects, and to use workspaces to hold collections of projects that may or may not go together.

Genome Workbench organizes your data into Projects. A Genome Workbench Project is a combination of data that semantically go together. Data inside a project can communicate more easily with other data inside the same project. For example, if you are reviewing a gene, it would be best to organize the data for the gene in one project, combining references to genomic sequences, transcripts, proteins, and any local analyses done on the sequence.

Workspaces are collections of projects. Workspaces provide convenient ways to organize sets of related data, such as a set of projects relating to all the genes you are studying in mouse, or presenting different chunks of data in different organisms.

What is the Project Tree?

The Project Tree is a view on your workspace and projects. The project tree shows you a hierarchical expansion of your data, and allows you to group data items into folders.

The Project Tree is available from the main menu at View -> Project Tree. It is on by default, and appears on the left-hand side.

What is the Selection Inspector?

The selection inspector provides a means for evaluating all the selected objects in Genome Workbench. The selection inspector has three modes of operation (Table, Brief Text, and Full Text), selectable by using the icons in the right-hand corner of the view. The modes are:

  • Table provides a tabular list of the most common attributes of selected objects.
  • Brief Text provides a short textual description of the selected objects
  • Full Text provides a verbose textual printing of selected objects; this mode implies the GenBank Flat File format for any selected features.

The strength of the selection inspector is in aggregating selections across views. The selection inspector features a drop down menu that indicates which view's selections are being shown. One of the options is to show selections from all views. This mode allows you to combine selections from the project tree with selections from any other view.

What is the Data Mining View?

The data mining view is a view that combines many modes of searching into one interface. From the data mining view, you can search for items in the public sequence repository; you can search for gene records from Entrez Gene; you can search for annotations in a given view; and you can search for patterns of sequences.

The data mining view is on by default, and is available from View -> Data Mining View. It is generally docked along the bottom.

How do I load data into Genome Workbench?

There are a few ways to do this.

First, you can Import data into Genome Workbench. Importing data allows you to load accessions from GenBank directly. Importing also allows you to read data from files. Import is available through File -> Import. You must decide whether you want the imported data to be loaded into a new project, or added to the current project.

Second, you can load data through the Data Mining View. In the data mining view you can search several public databases in Entrez (Entrez Protein, Entrez Nucleotide, and Entrez Gene) and load data directly from your query.

What data formats does Genome Workbench support?

Lots... The currently supported list of file formats for import includes:

  • FASTA sequence files
  • GFF2/GTF format (NOTE: GFF3 support will be added soon)
  • RepeatMasker .out format
  • Sequin-style 5-Column Feature Table format
  • Newick-format phylogenetic trees
  • Phrap/ACE assembly files
  • AGP sequence assembly files
  • NCBI ASN.1 objects (in ASN.1 text or binary or in XML format)

Questions About Specific Tools

Help! I'm trying to use a tool and I can't!

The most common problems concern selections. Genome Workbench expects that you have already identified the data that you wish to work with when executing a tool. For example, if you wish to BLAST a region of a genome, or to run ORF finder on a putative cDNA, you must identify the region of the genome or the cDNA first.

Genome Workbench makes extensive use of selections. Selections are visible in views, either by using dark background shading or by using a highlight box.

How do I run Blast2Sequences? I want to align some sequences that I have loaded into Genome Workbench.

You will need to select the sequences or ranges on sequences before you align. You may need to use the Selection Inspector to do this; in particular, pay attention to the drop down that indicates where your selections come from. You may need to use the option to select from All Views, particularly if you wish to combine selections from the Project Tree and another view.

Once you have selected your items, choose Tools -> Alignments -> BLAST Sequences from the main menu. You will receive a dialog providing the options for BLAST. In general, the defaults work well. You will need to clarify the query and subject sequences, as well as the BLAST program to run (such as BLASTp, BLASTn, MegaBLAST, etc.).

Can I run a BLAST search? How do I BLAST a sequence against the NCBI public database?

You can execute a BLAST search against the public databases using the tool at Tools -> Alignments -> BLAST Database Search. The dialog will walk you through

I've loaded some sequences. Can I run CLUSTALw or MUSCLE to generate an alignment?

Yes - support for CLUSTALx and MUSCLE is integrated into Genome Workbench. You can fid these in the Tools menu at Tools -> Alignments -> CLUSTALw and Tools -> Alignments -> MUSCLE. Genome Workbench will need to be able to find the binary to execute each of these programs. If you have installed the applications with CLUSTALw and MUSCLE available in your runtime PATH, then Genome Workbench will work out of the box. If Genome Workbench cannot locate the applications, it will ask you for their locations.

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