Pathema - Bacillus

Pathema- Tutorial

Pathema - Bacillus Tutorial
	Welcome to the Pathema - Bacillus Tutorial, an introduction on how to navigate the website for first-time users. The tutorial is broken into the following 4 sections: the Front Page, the Navigation Bar, Tool Usage, and Carts. Each section contains a brief description of the page along with screenshots of a representative page. Mouse over the boxes on each image to view more information on highlighted features. For more information on tools, see our Pathema Bacillus Manual page. If you are interested in our annotation methods, visit our gene naming and nomenclature conventions page.
	Front Page
	Home Page Highlights Box Find the latest information on Pathema - Bacillus tool and data releases in the Highlights box. Click on the links to see detailed information on the latest additions. Pathema - Bacillus class dates at JCVI are listed as well. Menu Bar Navigate the site using the drop-down menus. Click on the tab to view a more detailed description of the available tools in that section. *Search Box* Search through all Pathema - Bacillus annotation, genomes, genome properties, and Pathema - Entomoeba tools using this search bar. Featured Resources The Featured Resources section offers one way to easily navigate to the tools important to each topic. Click on a topic of interest to see genome specific tools and resources relating to the topic. Community Connections Links to additional Pathema - Bacillus resources, Community Resources and related external resources. Available Genomes Listed here are all available Pathema - Bacillus organisms. Click the organism of interest to see a list of all genomes available. From the list of all genomes click on a strain to go to the genome page. Contact Info Click on the 'Contact Us' link at the bottom of every page to contact us with questions, comments, and bug reports.
	Navigation Menu
	Organism Menu Go directly to the selected organism's Genome Page or to useful tools through the drop-down Organism menu. Drop Down Navigation Menu Navigate to any Pathema - Bacillus tool through the drop-down menus. For more detailed descriptions of a section's tools, click on the tab. History Navigation Displays a clickable history and path to a particular tool. Search Bar Quick search through all Pathema - Bacillus annotation, genomes, genome properties, and Pathema - Bacillus tools using this search bar.
	Tool Usage
	Many Pathema tools require users to make several selections to retrieve data. Below are examples of two common selections: organisms and role categories Selecting Organisms Select organisms from the Organism Selection Box: Click on the organism of interest. Double-click to add a single organism of interest to the Selected Organisms box. To highlight multiple organisms at once, press the Ctrl button. To find an organism, enter a part of or the full name, and click the 'Search' button. To reset the list, click on 'Show All'. Click the 'Add' button to add selected organisms of interest to the final selection box. Confirm that the selected organisms listed are correct. To remove an organism, highlight the organism from the Selected Organisms Box, and click the 'Remove' button. Use the 'Tree View' button to add organisms. Organisms are displayed in a taxonomic tree and can be added individually or in taxonomic groups.
	Organism Selection Box This selection box allows users to select organisms of interest. Double-click to add a single organism of interest to the Selected Organisms box. To highlight multiple organisms at once, press the Ctrl button. To find an organism, enter a part of or the full name, and click the 'Search' button. The reset the list, click on 'Show All'. Or, to view and add organisms individiually or in groups by taxonomy, click on the 'Tree View' button. Add/Remove Add highligted organisms from the Organism Selection box, or remove highlighted organisms from the Selected Organisms box Selected Organisms Box This box displays the list of selected organisms.
	Selecting Roles Click on the Main Role of interest. Click on the Subrole of interest. Click the 'Add' button to add selected subrole of interest to the final selection box. Confirm that the selected subroles listed are correct. To remove a subrole, highlight the subrole from the Selected Subrole Box, and click the 'Remove' button.
	Main Role Selection Box This selection box allows users to select a main role of interest. Selecting a main role will automatically populate corresponding subroles in the Subrole Selection Box. Subrole Selection Box. Select a subrole of interest to add to the Selected Subroles box. Double-clicking will automatically add a single subrole to the Selected Subroles box. To highlight multiple subroles at once, press the Ctrl button. Add/Remove Add highligted subroles from the Subrole Selection box, or remove highlighted subroles from the Selected Subroles Box Selected Subroles Box This box displays the list of selected Subroles.
	Carts
	The Pathema - Bacillus offers Genome and Gene carts for user convenience. The genome cart allows for pre-selection of a set of genomes of interest. All query pages will display only selected genome cart genomes in the selection box instead of all 30+ strains. Users can also add genes of interest to the gene cart while browsing the site from any page that displays genes. The entire cart can be viewed and downloaded at any time. Furthermore, genes in the gene cart will automatically be highlighted in all graphical displays on the site.
	Using the Genome Cart
	The genome cart allows for pre-selection of a set of commonly-used genomes. Selecting a list of genomes from the Genome Cart tool will automatically populate all selection boxes with only this list. To display the entire list when the cart has been selected, click on the 'Show All' button on the selection box. To clear the cart, delete all genomes in the Genome Cart selected genomes box. Genome Carts can also be edited at any time from the tool page..
	Select genomes Highlight genomes of interest. Add genomes Add selected genomes to the Selected Genomes Box Selected Genomes Box Displays the list of genomes to be added to cart Submit Selection Clicking on the Submit button will set the Genome Cart to your current list.
	After submitting, an alert box will appear to confirm genome cart selections. Click 'Ok'.
	Using the Gene Cart 1. Select genes to add from any page that results in a list of genes (Ex. All genes in with dnaa in the annotation)
	Add Genes Add selected genes to the gene carts (any checked gene). Use "select all" to check all genes. Select Genes Selects genes in the table one at a time.
	2. A confirmation box appears to confirm the addition of selected genes to the cart. Click 'Ok'.

	Viewing the Gene Cart Selected Genes appear under the 'Gene Cart' tool. Genes can be downloaded all at once or cleared from this screen.
	Edit Cart Genes Remove selected genes to the gene carts (any checked gene). Download All Genes Opens a tab-delimited text file of all genes and associated annotation.
	Genes placed in the gene cart are also highlighted in graphical analysis tools. In this example, the selected genes of subrole category 'Toxin production and resistance' are highlighted in the Protein Scatter Plot. A hit comprising of gene cart genes from both organisms will be highlighted in green. A hit comprising of a gene cart gene from the reference genome only will be higlighted in orange, and a hit comprising of a gene cart gene from one the comparison genome will be highlighted in purple.

Pathema - Bacillus Tutorial

Front Page

Navigation Menu

Tool Usage

Carts