Your project workspace has a single "directory" of taxonomic names with which you can identify specimens (and by extension media) or populate a matrix. You may load your taxa by hand, one at a time, using the taxon entry forms or in a batch process using a tab-delimited file from a database, Microsoft Excel or a similar application. For more information on adding taxa see the section called “Managing Taxonomy”.

Each distinct taxon is represented once, and only once, in your taxonomic directory. When you use a taxon to identify specimens and in matrices, you are doing more than just tagging those items with a taxonomic name. Rather, you are actually linking your specimens and matrices to a taxonomic concept. If you subsequently change the taxon, your changes will automatically propagate to all of the specimens and matrices that reference the taxon.

As with taxa, your workspace has a directory of specimens that are referenced in your project. Specimens can (and should) be associated with a taxonomic identification. They may also be depicted using uploaded media.

There are two types of specimens: vouchered and unvouchered.

For vouchered specimens – specimens from a formal collection – you must at a minimum provide an institution code and catalog number for each specimen. Both of these values should conform to the standards of the institution from which the specimen originates. If you are not sure of the formats for these values, contact the institution's collections manager. Typically, the institution code will be a 2-4 letter abbreviation of the institutional name (e.g., AMNH = American Museum of Natural History, YPM = Yale Peabody Museum). Whenever possible a collection code should be provided. As with the institutional code and catalog number, this should conform to institutional standards. Many, but not all, institutions use collection codes.

Unvouchered specimens are those obtained from sources other than formal collections, including literature and the Internet. You are encouraged to provide detailed notes about the origins of the specimen in the "notes" field. You can also attach a formal bibliographic citation to a specimen.

A taxonomic identification of the specimen should be provided for all specimens. The identification is used by MorphoBank's matrix editor to retrieve relevant media, and by the search/filtering system to organize your media. Unidentified specimens will be much less useful than identified ones.

Figure 2.2. A vouchered specimen

Figure 2.3. An unvouchered specimen

You can upload any number of media documenting specimens to MorphoBank. Most uploaded media are images, although video and audio formats are also supported. (Thus our use of the more neutral "media" terminology).

You will typically upload an image and tag it with a specimen identification, any pertinent copyright information and a view description (eg. "dorsal", "lateral", "palatal").

MorphoBank accepts a variety of image formats including JPEG, GIF, PNG, TIFF and Photoshop. Note that Photoshop files that use layer effects may not render properly on MorphoBank. For consistent results we recommend converting these files to TIFF format before uploading. All image files should be in RGB mode. Files in CMYK mode may not render properly.

You should upload image files at the highest resolution that makes sense for your project. MorphoBank will automatically create sized versions for use on the site as well as a full-resolution version optimized for online viewing. The original uploaded file will be retained and can be made available for download.

MorphoBank also accepts the following video file formats: MPEG-4, QuickTime and WindowsMedia. The preferred video file format for upload to MorphoBank is MPEG-4. Files in QuickTime and WindowsMedia format will usually work so long as the compression method used is supported by MorphoBank's video processor. In general, videos compressed with WindowsMedia will work, as will most QuickTime compression methods (some very old and rarely used methods like GIF compression are the notable exceptions). AVI files usually will not work and should be converted to MPEG-4 prior to upload. In general if your uploaded file is being rejected by MorphoBank it is recommended that you try re-encoding the file in MPEG-4 format using one of the many video conversion tools available for Mac OS X, Windows and Linux.

Audio files may be uploaded to MorphoBank in MP3, AAC, AIFF or WAV format. Other formats are not supported. If you need to convert or edit your audio files use a sound editing application such as Audacity (http://audacity.sourceforge.net/).

MorphoBank does not support the PowerPoint file format. If you need to upload images from a PowerPoint presentation, you should export them from PowerPoint in a supported format such as JPEG and then upload those files.

Media may be uploaded one file at a time using the "Add new media file" button. For large numbers of files, the Batch Media Upload tool may be more efficient. It is accessed with the "Add media batch" button and allows you to enter all the information on the standard media form for a group of media files that are uploaded as an archive in either Zip or Tar format. For more information about using the Batch Media Upload Tool, including how to prepare you archive for upload, see the section called “Batch uploading media with the Batch Media Upload Tool ”.

Figure 2.4. Add Media Buttons

Project members may create, edit and publish phylogenetic matrices using MorphoBank's matrix viewer/editor application. A matrix's axes are composed of characters (see the section called “Characters”) and taxa (see the section called “Taxonomic names”). The cells of the matrix contain character states and, optionally, media (see the section called “Media”) with (also optionally) labels. Labels applied in a matrix cell are specific to that cell and automatically include text describing the cell's character and taxon. Cells may also have attached bibliographic references, member comments and research notes.

You can start a matrix from scratch and populate it solely using the MorphoBank matrix editor or you can use an existing NEXUS format file as a starting point. Regardless of how you begin, you can import the contents of additional NEXUS format matrix files (produced by applications like MacClade or Mesquite) into your MorphoBank matrix at any time. All taxa and characters that do not already exist in your project will be automatically created when the file is imported, and states for existing taxa/character pairs merged with the existing data.

In projects with multiple matrices taxa, characters and media are shared across all matrices in your project. A change made to a taxon, character or media item in one matrix, or in the item-specific editing screens, will instantly be reflected in all matrices where the item is used.

It is possible to download your matrix from MorphoBank as a NEXUS or TNT file at any time. The file will include all characters, taxa, cells and notes, but not images since they are not formally supported in the NEXUS or TNT format. Images can, however, be downloaded as a zipped folder to the desktop by clicking on the "Download Project" link on the Project Overview page. The archive will contain SDD XML format data files with associated matrix, character, taxon and specimen data. Note, however, that these images will not be viewable associated with cells in desktop programs reading the NEXUS or TNT file.

Figure 2.5. Matrix editor/viewer

As with taxa, your project has a single directory of characters and their associated states. Each distinct character is represented once, and only once, in your project's character list. When you use a character in a matrix, you are doing more than just bringing in the character's name. Rather, you are actually linking a characteristic concept to your matrix. Consequently, if the character is changed in one place, the change will propagate to all other places where the character is used.

Unlike taxa and other deposited data, characters cannot exist independently of matrices. That is, to exist in your project at least one matrix must reference the character. Put another way, if you delete a matrix all characters referenced only by that matrix will be removed as well.

A character may have as many states as required. Each state has an associated name and number, as well as any number of exemplar images. Images may also be associated with the character independent of a specific state. Characters may also have bibliographic citations and member comments attached.

Any number of documents can be added to a project. Documents may be in any format, and can document aspects of the project or provide data in formats that are not directly supported by MorphoBank. Each document may include an optional title and description, and may be published along with other data (media, matrices, etc.) or kept private to the project.

When a project is published, all documents with a "publish when project is published" status will be listed and made available for download on the project's MorphoBank project page, accessible from the project browser and through the site search.