BioCoRE - Biological Collaborative Research Environment

We are continually adding new features to BioCoRE (and expanding the spotlight to highlight more of the existing features of BioCoRE) so visit often. We also encourage you to take our tour for more information.

You can set "watches" on folders in the BioFS and be notified via email when files are added to the folder. This can be convenient in DropBox situations when someone leaves you a file, for instance. You can also set up email watches for Lab Book, BioLog, and VMD saved state entries from the "Utilities" menu.
Email watch
BioCoRE can be used to post quizzes and polls for your project associates. The poll creator can choose start times, end times, and other aspects of the poll, and then users will get a poll window via their Control Panel where they can answer the question. Quizzes actually have a correct answer designated, so that BioCoRE can automatically score responses.
[Polls And Quizzes Within BioCoRE]
The BioCoRE Control Panel normally provides chatting by project. However, you can also hold private chats with members of your project. These chats appear in separate tabs that you can switch among for all of your private chats. When done with a private chat, that tab can simply be closed.
[Private Chatting Tabs In The Control Panel]
The BioCoRE Control Panel can solve mathematical expressions for you directly from the chat window. Trigonometric and log functions are supported, as well as random numbers and summations. As useful values are calculated, they can then be cut and pasted for everyone in the project to see.
[Math In The Control Panel]
The BioCoRE Control Panel allows you do Google searches directly from the chat window. The top ten responses are given, which include the title of the destination web page as well as its URL. As useful sites are found, they can then be cut and pasted for everyone in the project to see.
[Google Searching In The Control Panel]
BioFS, the BioCoRE shared filesystem, can be accessed from your computer's desktop in the same way that you access a folder on your hard drive. By using WebDAV technology, the files appear local but are actually the same files that you share with your collaborators. You can run your favorite applications on these files and the most recent version is automatically available to your collaborators.
[BioFS Icon On Desktop]
Do you want to be able to share some of your research information with the world? In addition to creating private projects in BioCoRE, you can also create public areas. The project creator can decide which areas of the project are public and these areas can then be viewed by anyone with a BioCoRE account.
When you post a message to the BioCoRE Message Board, you have the option of selecting a checkbox at the bottom of the page, which will send email to your project members. This is an easy way to contact other project members, even those not currently logged in to BioCoRE, while simultaneously archiving your message in the BioCoRE notebook.
[Email Notification Option Checkbox]
The BioCoRE Job Manager assists you in monitoring and logging computational jobs. You tell BioCoRE about your accounts on supercomputers or local machines, and BioCoRE keeps track of the account information for you. Then you can submit runs to those accounts using a simple web-based interface by just filling in a form. As the jobs run, their progress is monitored and reported to you, and after completion, job details are available for easy reference.
[Job Manager Webpage]
Each BioCoRE project has a Lab Book where project members can keep a journal of their research progress. The lab book entries are automatically sorted by user and can be viewed and searched by all members of the project. Entries can be "deleted" from the main view but are still available, which makes it easy to determine exactly when something occurred.
[Lab Book Webpage]
BioCoRE includes the BioFS, a shared filesystem. You and your collaborators can use the BioFS to share files. As an example, if you are working on document, you can put it in the BioFS and your collaborators can then easily download it. In addition, some tools, such as Job Management, place files in the BioFS for easy access.
[BioFS Folder View In Webpage]
BioCoRE allows users to let others know their current tasks, upcoming schedules, project roles, and biographical information. In addition to informing others, this is helpful in determining the state of a project. Select "Project->User Information" from the Control Panel menu to edit and view user profiles.
[Current Task List]
The BioCoRE Control Panel is designed to stay running on your desktop as you do your daily work. It will automatically notify you (via visual and audio cues) when: your collaborators log in/out, send text messages, post new notebook entries and more.
[Control Panel Menu and Chat Window]
Each BioCoRE project has a Link Library where users can store web links to interesting websites. This gives each project a shared "Bookmarks" file where one project member can post a link to a useful website, and other project members can automatically access it.
[Link Library Webpage]
BioCoRE uses JMV, a browser-based Java molecular viewer, which allows you to quickly view molecules in different representations and color schemes. You can use JMV to view PDB files stored in the BioCoRE Filesystem by clicking "View this molecule using JMV" in the file's "Properties" window.
[JMV Logo]
BioCoRE enhances VMD by making it very easy to share molecular views with collaborators. Once you have a desired view in VMD, the view can be saved back to BioCoRE by selecting an option in a special BioCoRE window. Collaborators can then use BioCoRE to load the same view in their own copy of VMD.
[View Of Pub/Sync Window in VMD]
The BioCoRE Control Panel is run using Java Web Start. Java Web Start is a package from Sun that lets you run applications independent of a web browser. This means that the Control Panel will stay active even if your web browser crashes or closes.
[Java Web Start]
BioCoRE can be accessed via a handheld PocketPC-based PDA, such as the Compaq iPAQ. A researcher using an iPAQ, equipped with access to the internet (via wired or wireless ethernet or modem), can access BioCoRE and perform most of the same functions that he or she can perform sitting at a desktop computer.
[Job Manager Page Running on a PDA]
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