General Questions:

Installation Questions:

Interface Questions:

Specific Tool Questions:

Data and View Questions:

Editing Package Questions:

BAM File Questions:


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.

What platforms does Genome Workbench run on?

Genome Workbench runs natively on Windows 2000/XP/Vista/Windows 7, MacOS X (10.6, 10.7), and Linux (Ubuntu 10.04 LTS). Other flavors of Linux are supported through compiling from source files available for download. We provide binary snapshots of the application for Windows and MacOS X (Intel only); the source snapshot can be used on any platform.

What network settings are required for Genome Workbench?

In order to function Genome Workbench requires network conection. In most of the cases you do not need to perform any special network set up activities. Each time Genome Workbench starts it performs automatic configuration, detecting your network settings and adjusting for best performance.

Genome Workbench provides best experience when connected to fast and stable land line network. It might be able to work with mobile environments (such as cellular modem) but it is designed for best results in stable environments (such as your office or home networks). If you are a mobile user and start the work in one environment (say office), then suspend and continue in a different environment (say home), Genome Workbench will try to adjust to a changed environment. If adjustment does not work you might have to restart Genome Workbench.

If automatic configuration does not give you the desired result (in case your network settings are very uncommon) you can search for more information and instructions at https://www.ncbi.nlm.nih.gov/IEB/ToolBox/NETWORK/firewall.html

That page is particularly useful for network administrators.

Please communicate your uncommon settings to the Genome Workbench development team through one of the mailing lists (see below) so that the situation is taken care of in one the future releases.

What is the best way to provide feedback?

gbench-bugs@ncbi.nlm.nih.gov. This is an e-mail alias for reporting bugs with Genome Workbench as well as communicating any other feedback. This alias is the recipient of all feedback reports supplied by Genome Workbench.


Installation Questions

I have installed Genome Workbench, but it will not 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 => Options. There are two tabs in the dialog that appears; select the tab for Network Connection
  • There are two radio 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, depending on your firewall 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. gbench.ini contains a set of settings that are common enough that most firewall users should be able to work with. This file should be placed in your Genome Workbench user-specific directory:

  • Windows: C:\Documents and Settings\<login name>\Application Data\GenomeWorkbench2\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.

Can users install Genome Workbench on Virtual Machines?

Genome Workbench can be installed on any machine including virtual, but VM installation can create certain problems with access to Graphics card (GPU) and OpenGL. GPU is a real resource that is used for OpenGL visualization. Some virtual machines in certain circumstances do not provide access to GPU or OpenGL. The user has to configure the VM in a way that such an access is granted.

Can I use Genome Workbench with Windows Remote Desktop?

Yes.

Can I use Genome Workbench with X Window System?

Yes. We tested and recommend X2Go as a terminal server software. Please refer to Running Genome Workbench over X Window System manual.

Can Genome Workbench be installed on an HPC Cluster running on Linux?

Yes. Please refer to Running Genome Workbench over X Window System manual.

What should I do if Defender prevents from installing Genome Workbench on Windows?

You can still install Genome Workbench, follow the instructions.

Can I run Genome Workbench on Google Cloud or Amazon Web Services platforms?

Yes. Please refer to Running Genome Workbench over X Window System manual.


Interface Questions

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 corresponding HGVS coordinates and the franking 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?

FAQ 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 Broadcasting and how to use it?

Broadcasting is a powerful and unique feature within Genome Workbench that allows the sharing of selected objects between multiple active views. Users interact with the currently focused view, and that view lets the other open views know what is happening. Depending on the context, views can broadcast sequence ids, selected locations on molecules, visual ranges, nodes of trees, etc.

Other open views listen for these broadcast events and may respond by highlighting relevant objects, such as sequence ids. If two open views are of the same type, e.g. graphical sequence views open on the same molecule, the non-focused view can ‘follow’ the current selections and visual range of the active view. This is especially useful when views are configured to show different characteristics of the molecule such as different tracks, different zoom levels and/or different display options.

Broadcasting is also supported between phylogenetic tree views. This can be very useful for finding similarities or differences between two open trees. Clicking on nodes or selecting groups of nodes in one tree will result in matching nodes, such as nodes with matching sequence ids, being highlighted in the other tree.

Control various broadcasting options with the Tools=>Broadcast Options Dialog.

Broadcast options dialog

Inspect and use current broadcast selections with the View=>Selection Inspector view.

View broadcasting in selection inspector

The Selection Inspector is useful because you can see what is selected on each view in one place and you can run tools (like BLAST) on objects and locations subsequently picked from this selection set.

What is the Selection Inspector?

FAQ 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 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 Search View?

FAQ data mining view

The search view is a view that combines many modes of data mining into one interface. From this 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 Search 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/GFF3 format
  • iUCSC-style BED and WIG files
  • Newick-format phylogenetic trees
  • AGP sequence assembly files
  • NCBI ASN.1 objects (in ASN.1 text or binary or in XML format)

Specific Tool Questions

Help! I am trying to use a tool and I cannot!

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 => Run Tool => 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 => Run Tool => BLAST Database Search. The dialog will walk you through

I have loaded some sequences. Can I run MUSCLE to generate an alignment?

Yes - support for MUSCLE is integrated into Genome Workbench. You can find these in the Tools menu at Tools => Run Tool => 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.

How do I get the application to it's default setting?

In order to reset application to default settings for Graphical Sequence View you need to:

  1. Close Genome Workbench
  2. Delete the %appdata%\GenomeWorkbench2 directory (Windows) or $HOME/.gbench2 directory (for Linux) or $HOME/Library/Application Support/GenomeWorkbench2 directory (for MacOS)
  3. Restart Genome Workbench

Data and View Questions

What types of data can Genome Workbench show?

Genome Workbench can show sequences and alignments.

What types of views can I display for a sequence?

For a sequence Genome Workbench can display:

  • Feature Table View
  • Graphical Sequence View
  • SNP Table View is no longer supported

What types of views can I display for an alignment?

For an alignment Genome Workbench can display:

  • Alignment Span View
  • Alignment Summary View
  • Cross Align View
  • Dot Matrix View
  • Multi-pane Cross Alignment View
  • Multiple Alignment View
  • Tree View

What types of views can I display for any type of data?

Views that Genome Workbench can display fo any type of data are:

  • Generic Table View
  • Sequence Text View
  • Text View

Can I display multiple views for the same data simultaneously?

Yes, Genome Workbench can display as many views as you want, even several views of the same type.

How can I set default view for my data?

In the "Open View" dialog each view available for your data has a Make Default link on the right. Just click on that link, and that view will be marked as default, and will be displayed when you double-click on the data. If you want to change a default view - just select another one, it will be selected and the old default deselected.

Where can I find more information on views?

For more information on views please see the Working with Multiple Views Tutorial.

Editing Package Questions

Why would I want to use the Editing Package?

The Editing Package allows you to create a new submission for GenBank by converting and combining your existing data files into the correct format, identifying missing information and errors in the data, and providing you with tools to correct and augment your data.

What kind of GenBank submissions can I prepare with Genome Workbench?

Currently, you can prepare submissions that contain the genome for a single biological sample – the organism name and other qualifiers that identify the organism (strain, isolate, breed, etc.) and the sample collected (collection date, country where the sample was collected, etc.) must be identical for all sequences in the submission. The submission could contain a single sequence, for example, an entire chromosome, or multiple sequences, where each sequence represents a complete chromosome, plasmid, or organelle, or the submission could represent a Whole Genome Shotgun (WGS), where some or all of the sequences represent parts of a chromosome, plasmid, or organelle. Later versions of Genome Workbench will permit the user to create and edit submissions with sequences from different organisms or samples, such as population studies or phylogenetic sets.

How to start GenBank Submission with Genome Workbench?

Follow the introduction or watch the Video (link TBD).

I built an ASN.1 file using some other tool. Can I edit it with Genome Workbench?

Yes! Genome Workbench can read and write ASN.1 data, and will provide the same analysis of missing information and data errors whether you start with FASTA or ASN.1.

What if I don’t want to submit my data to GenBank? Can I still use Genome Workbench to look at it and make changes?

Yes! You can use Genome Workbench to review and edit data that you do not want to submit; your data is private until you decide to submit it.

Is this like Sequin?

Yes, but better! While not all of the functionality of Sequin is present (for example, you cannot yet prepare submissions with sequences from different biological samples), Genome Workbench can serve a similar purpose, and will be expanded to replace more of the Sequin functionality in later releases.

BAM File Questions

Does Genome Workbench support BAM/cSRA formats?

Yes, Genome Workbench can open use BAM and cSRA formats. Genome Workbench can use local BAM/cSRA files or stream it from the WEB over http(s) protocol.

How does it work if BAM reads use UCSC chromosome names and not NCBI accessions?

Genome Workbench connects to a NCBI genome collections service and uses names mapping to map chromosome names in BAM files to NCBI accessions and show BAM reads in Graphical Sequence View.

How can I visualize BAM files on non-NCBI genomes?

You need to load FASTA files into the project and then connect the BAM file. If sequence ids in BAM file refer to sequence ids known from FASTA - it will show in Graphical Sequence View.

Where can I find more information on Genome Workbench working with BAM files?

More information can be found i Working with BAM files and Exporting BAM/cSRA Coverage Graphs as WIG Files online tutorials as well as Import BAM and Export Selected Alignments video tutorial.

Support Center

Last updated: 2019-08-14T21:00:34Z