Help for Project Summary Page
In the projects index page, when you click on a project title, you will be taken to the Project page. This page shows a list of experiments for the project, and a side-bar menu to navigate through the detail of the project. The initial state of this page might look something like this (shown here using the demo project):
On this page the top is the same as before: the toggles for Projects and Published data, a search interface, the help button, the Report Issue Button, and the user-action pull down menu (which we already encountered in the description of the top level Projects Page).
The left side panel shows the project parts and actions: the Project title (which is a button that will return you to this page), the Project Description, the list of people sharing the project, the Notes/To-dos panel, the Project-Datasets panel, the Experiments list opener (with the number of experiments), the Samples panel, the Files panel, the Settings panel, the Sync button, the Globus Commands, and the Shortcuts list. See the section "Left Side Navigation Bar", below.
Just to review, In the upper left corner of the page, the Materials Commons buttons are used to navigate to the top level pages of the site. Clicking on the 'Projects' link will return you to the top level of the Project management area of the site Projects Index Page. Clicking on the 'Published Data' link will take you to the top level Public Data Page.
Next to the these top level navigation links is the "Search Project..." text entry. To search just type some part of any name in the project (for example, part of a sample name). When you hit return the search index will retrieve those object (Files, Samples, Experiments) that match the search string. To reset the search, click on the project title at the top of the left-side navigation bar, or refresh the page in the browser.
On the right side of this banner is the User Action pull down menu (which we encountered in the help on the Projects Index Page), and a link to report issues. When you click on the link to report issues, your default mail application should open with a message addressed to help@materialcommons.org. Use this to report any problems that you are having. When you report a problem, please try to be as detail as possible about what you were doing at the time, what went wrong, and what you expected to happen instead. Obviously, if your message says something like "it doesn't work", we can't be of much help.
The '?' icon links you to these help pages.
The navigation bar, on the left, starts with the name of the project, which is also a "home" button; clicking on it will bring you back to the starting page, that is the list of experiments, shown above.
In addition, this navigation bar contains the following items:
Select this item to chance the project description: type a new description and click Save; or click Cancel
Select user with whom you wish to share this project. Any user selected becomes a co-author on the project. That person will be able to edit any part of the project and carry out any action on the project that is permitted to the owner of the project (except "delete the project"; only the owner of the project is able to delete the project).
Use these interfaces to add notes and do-to items to the project. For the to-do items, click "ADD TO-DO" and type the text for the item; delete the item, mark it Done, or check it off the list. For notes, click "ADD NOTE" and type the title and content of the note in the right side edit panel. Click "DONE" to save the note. For the text of the note, styling with GitHub markdown is supported; click the "Styling with..." link to see markdown docs.
A data set is a collections of project experiments, samples, and file, intended for publication. You can create datasets at the Project or Experiment level. Once published, a dataset becomes world readable and appears in the Materials Commons "Published Data" list. A dataset can be un-published and deleted. A published dataset can not be deleted. An unpublished dataset that is not deleted can be republished.
Use this interface to see your list of Project datasets, and select then for editing. Published dataset can not be edited. To edit a dataset un-publish it first. To add an new dataset, click "ADD DATASET". When you add a new dataset the Initialize Database panel will appear:
Set the name of the dataset, then select the experiments you want covered by the dataset (EXPERIMENTS tab). and then select the samples from those experiments that you want covered by the dataset (SAMPLES tab). This initial selection will determine what experiments are used for the source of samples, processes, and files, for the dataset. And when set of samples are initially offered as a the ones involved in the selected processes. These selections can be changed later in the dataset edit panels.
When you initially add a dataset, it will be displayed in the dataset list, as shown above. In our example, the Demo Dataset was added and it appears in the list of datasets. Click on the dataset name to open the initial dataset edit panel:
At the top of the panel a button to "SAVE CHANGES" to the details of the dataset, a button to "CANCEL" the edit, and a button to "PUBLISH" the dataset.
In this edit-details panel you can set the details of the datasets metadata: name (rename), description, institution, funding, license, tags/keywords (comma seperated), authors, and releted papers.
You can also add a DOI to the dataset. Once you have added a DOI to a dataset, it can not be deleted. It can be unpublished, and this will remove it from the published dataset list, but the DOI requires that the we keep the dataset record, so it can not be deleted. If someone follows the link from the DOI to an unpublished dataset, they will see a message to the effect that the dataset is unpublished, most likely because it is being edited by the owner, and to check back later.
Once you have set the desired values be sure to click "SAVE CHANGES" at the top of the panel.
The tabs: Details, Samples, Files, will take you to the those panels in the edit panel.
The Edit Samples panel lets you select, and add or remove samples from the dataset. Be sure to "SAVE CHANGES" before leaving the panel, or "DISCARD" the changes made to reset.
The Edit Files panel lets you add files or remove files from dataset.
The Experiments button in the left-side menu shows the number of experiments. If you click on it you will see a popup-menu of the list of experiments. Click off the menu to close it, click on the menu to select an experiment. We will cover the details of the Experiment editing options in a separate set of help pages. See Experiment Page in the Experiment Page and Panels part of the Help pages.
This panel contains the selection of experiment state, the experiment actions, and a list of experiments. On at the top of the experiments-list panel field is a set of radio buttons that filter Experiments by activity state. When we look at details panel of the Experiment page, you will see that an Experiment can be in one of three states: Active, Completed, or On Hold. By default, you are viewing only those Experiments that are active. To view Experiments in other states, click the corresponding radio button.
Finally there is the Create New Experiment button which we will cover in the next section.
The 'Start New Experiment' button will do just that. When you click on it, you will see the Create Experiment dialog.
Where you set the name and description of the new experiment. Only the name is required (the description being optional). Any additional values for the Experiment are set in the Experiment page itself, discussed in the section on the Experiment Page. You will also be able, on that page, to edit the Name and description. Clicking Submit on this dialog, takes you directly to the Details Panel of the newly created experiment.
Creating a new experiment also effects the Project summary display. The experiment will be listed in the list of experiments for the project.
Once created, the experiment appears in the "experiment card" display in the Project page (shown directly above). Each card contains a summary of the main attributes of the Experiment description: the title; the description; the date/time the record was last updated; the numbers of Publications, Samples, Processes, Datasets, Files and Notes in the Experiments record; and the Description of the experiment.
Clicking on the Experiment card takes you to the Experiment Page.