The Recipe Resource is a repository for GenomeSpace recipes - short, standalone workflows for completing complex bioinformatic analyses. Recipes use GenomeSpace-enabled tools and data resources to demonstrate integrative analysis, walking users step-by-step through the process of obtaining and analyzing data. The Recipe Resource homepage functions as an access portal to recipes and recipe-related content, such as documentation for using and developing recipes.
The content of the Recipe Resource homepage is organized into the following categories:
The Recipe Resource list is the list of all currently published recipes. This is the portal to reading, browsing, searching, and filtering all published recipes. The following explains how to navigate the recipe list, in order to find the recipe that best suits your interests and analysis needs.
When logged in, a GenomeSpace user will see a login navigation menu allowing access to features of the Recipe Resource. The house icon will return the user to the recipe homepage. The My Recipes icon allows users to access the recipes they have created. Here, users can add, edit, or delete recipes, or re-order the steps in the recipes.
Users can also search through the published list of recipes by using the search bar. If users have searched for a specific term, limiting the number of recipes displayed, they can re-set the list to show all recipes by clicking the List All button.
Each recipe listing has a descriptive title of the analysis, e.g. "Build and visualize a module network using putative aberrant regions and expression data". Each title is accompanied by a graphic depicting the tools used in the recipe (e.g. Galaxy and GenePattern). Each recipe has a short description of the basic input and analysis of the recipe, which can be accessed by clicking on the recipe title box to expand or collapse the short description. Clicking on the recipe title will re-direct the page to the recipe itself. To see all the recipe descriptions, click the Expand all recipe descriptions link. Once expanded, the link can be used to collapse all recipe descriptions, as well.
Recipes are tagged with certain information to make searching and filtering recipes easier. Recipes can be filtered by tags, which are categorized into several types:
To filter the list of recipes by tags of interest, select the tag that you are interested in filtering by. For example, if you want to find all recipes utilizing GenePattern, click on the GenePattern tag under the Filter by tool category. The list of recipes is automatically updated based on the user selection of tags. More than one tag can be selected both within and between categories.
Within a category, multiple tags can be selected by either clicking and dragging, or by using ctrl+click to select tags. Selecting more than one tag within a category will filter the list of recipes as an inclusive or query, e.g. selecting both the GenePattern and Cytoscape tags will reduce the list to recipe utilizing GenePattern OR Cytoscape. If a recipe uses both tools, that recipe will be included.
Between categories, if multiple tags are selected the list of recipes will be filtered as an and query. For example, selecting GenePattern from the list of tool tags and RNA-Seq from the list of data tags, will filter the recipes to include only recipes that utilize GenePattern AND feature RNA-Seq datasets.
Filters can be combined across datasets in a similar way. Selecting the GenePattern, Cytoscape, and RNA-Seq tags results in a list of recipes that utilize (GenePattern OR Cytoscape) AND feature RNA-Seq data.
To clear the filters, click the clear button.
Recipes are short, standalone workflows describing the steps necessary to complete a common bioinformatic analysis, such as quality-checking RNA-Seq data, building a network from a list of genes, or identifying differentially regulated genes. Recipes usually feature two-three GenomeSpace-enabled tools or data sources. They can be used sequentially to create a longer or more complex analysis.
Recipes can be navigated to using the recipe list, or by using the search box on the Recipe Resource home page. There are several features on recipe pages to help users understand and utilize the recipe content.
Each recipe features a header, which lists metadata about that recipe. For example, an image accompanies the title, illustrating the tools used in the recipe. The date and author of the recipe is listed. A GenomeSpace cloud icon ( ) indicates 'official' recipes that have been created by the GenomeSpace team. Underneath this, tags for data type and analysis type are listed for each recipe. Finally, each recipe features a rating system where users can either upvote () or downvote () the recipes to give feedback on recipes. Ideally, users will also comment on the recipe to leave questions, or feedback about the recipe quality or utility. However, looking at the upvotes and downvote on a recipe allows a user to quickly judge if that recipe is considered useful by the GenomeSpace user community. Only logged-in users can upvote or downvote recipes.
Recipes have a dynamically-generated navigation menu. Users can click on individual items of the navigation bar, to automatically jump to that part of the recipe page. The navigation menu will scroll with the user. The navigation menu will display the top-level links for each section of a recipe. In the case of recipe sections that have sub-headings (e.g. the Steps section of a recipe) the navigation menu will expand to list the sub-steps once the user has reached that section of the recipe. Upon moving to a different section, this will collapse to hide the extra sub-headings. The Back to the Top link allows the user to jump to the top of the recipe page at any time.
The brief description of a recipe step is always displayed to the user. However, due to the amount of content, the step-by-step instructions and the videos are contained in collapsible/expandable boxes, for ease of use. To expand or collapse a step, a user should click on the step box to toggle it. To expand or collapse all the steps, the user can click on the Expand All Steps or Collapse All Steps buttons.
Step-by-step instructions for recipes will feature screenshots. These screenshots usually depict the interface of the tool being used, and contain highlights or other indicators to help users understand the parameters being changed in the interface. In addition, the detailed step-by-step instructions accompany the screenshots. For steps with videos, the video is embedded into the webpage. For individual steps, the videos are short for ease of viewing. If a user is interested in viewing all of the videos in a recipe, there is a video playlist featured at the top of each recipe. This is a YouTube compilation of the individual videos, which can also be watched on the GenomeSpace YouTube channel.
GenomeSpace users are encouraged to comment on recipes and leave feedback about the recipe content. If logged in, users can type a comment into the Content box, and click the Submit Your Comment button to submit the comment. The comment will be logged with the date, time, and author's GenomeSpace username. Users are invited to ask questions about recipes, suggest alternative parameters or analyses, suggest improvements to recipes, and leave other feedback for the GenomeSpace team.