Workstations
Workstations throughout the physical facilities of IGSP run Linux, Mac OS X, and Windows operating systems, with the primary platform for computational biology being Linux. Four full-time staff maintain servers and workstations.
Linux Desktop
The default Linux desktop environment is standard Fedora-flavored GNOME, though KDE is also available, and the pure-of-heart (or masochistic) can use a simple window manager in X.
Because IGSP Linux workstations use the network to handle "home" directories, your desktop setup folllows your log in, and it isn't tied to a single machine.
Word processing, spreadsheets, and presentation software. Open Office, the open source response to Microsoft Office, is quite good in providing word processing, spreadsheet, presentation, and (soon) database applications. Many documents created in Microsoft Office can be opened and edited in Open Office, though documents that contain complicated tables and images are less likely to make the move into Open Office intact. Open Office also exports documents in Office formats, with about the same level of success as importing them.
Email. Text-based pine is available, and Ximian Evolution is the GNOME default. Thunderbird is also available.
Web browsers. Mozilla is the default, though Firefox and, for a while, Galeon are available as well.
Unix shells. The default shell is bash. It is possible to have the shell changed to tcsh, though people need to have the system administrator make this change. (That is, chsh won't work.)
Useful Links:
Mac OS X Desktop
Problems that were noted with the "Tiger" Mac OS X version (10.4) have been resolved in recent updates, so IGSP supported Macintoshes can run Mac OS X "Tiger" without a problem, though some configuration may need to be completed by a member of IGSP IT staff.
Security applications. Although it is not required, use of the Mac OS X firewall feature is recommended. Mac OS X uses the firewall by default at installation. More important for workstation security is the currency of the operating system and applications, and Mac OS X includes an automatic update feature. For people who have administrative privileges on their Mac OS X machine, this updater should be set to run daily.
Presently Macintosh computers are less frequently a target for security exploits than computers running Windows. But it's worth knowing that the main threat to Mac OS X workstations comes from choices that computer users make, not from "automatic" worms and viruses. In general is is best never to click on a link that appears in an email message, even if you know the person who is listed as the sender of the message. Only open email attachments that you are expecting to receive.
Word processing, spreadsheets, and presentation software. Microsoft Office is the de facto standard, and with good reason. Office is a very good productivity package that includes Word, Excel, and Powerpoint. Duke's site license makes the applications very affordable.
When sending Word documents to others, it is wise to include versions of the document in some format other than Word. The PDF format renders documents quite well, and the Adobe Acrobat reader is free for people to download. It is also available for most operating systems, while Microsoft Office is not.
Lotus Notes & other email clients. The Duke Health Enterprise has standardized on Lotus Notes. Depending on the specific role you have in the system or the people you most frequently interact with, you may find Lotus Notes a good choice. However, many people have chosen not to use Lotus Notes, preferring instead to manage messaging and calendaring in other ways. The University technology group (OIT) recommends Mulberry as the email client. The Mac OS X "Mail" application is a very good option, too. Eudora may or may not work for you, depending on how your logins are set up. (Authentication is required for both receiving and sending emails, and Eudora makes the assumption, usually correct, that logins and passwords for these actions are identical.)
The Notes application is set up by a system administrator.
Web browsers. The recommended web browsers are Safari (included in the Mac OS X operating system) or Firefox which is a very useable and promptly updated application. It is open source software and is free to download. Unless a web-based application requires it, we ask people not to use Microsoft Internet Explorer. Some applications, most notably the Duke Health Enterprise's "eBrowser," require IE running on Windows. If "eBrowser" is a critical application for you to use, you will need to use Windows XP.
Meetingmaker. For people who do not like Lotus Notes for calendaring, another product is available. Meetingmaker runs on Windows and Mac OS X platforms. The Meetingmaker server is operated by OIT.
Useful utilities. The following applications are site licensed for use by Duke students and staff (licensing details vary, however). They can extend the usefulness of Mac OS X-based workstations.
- MacSFTP provides a graphical interface for secure file transfers.
- X11 is a graphical environment for many Unix applications, and it allows you to use a Macintosh as a terminal on a Unix server running the X Window system. X11 is part of the standard Mac OS X installation.
- EndNote is bibliographic citation software that is well integrated with Microsoft Word.
Windows Desktop
IGSP Windows machines run Windows XP SP2 and there are certain other required applications that help to improve the security of the Windows machines.
Security applications. The IGSP HIPAA security policies call for all Windows workstations to have functioning and updated virus detection software. McAfee is freely available by Duke site license. The license also covers the daily virus definition updates. Although it is not required, use of the Windows XP firewall feature is recommended.
It's worth knowing that the main threat to Windows workstations comes from choices that computer users make, not from "automatic" worms and viruses. In general is is best never to click on a link that appears in an email message, even if you know the person who is listed as the sender of the message. Only open email attachments that you are expecting to receive.
Word processing, spreadsheets, and presentation software. Microsoft Office is the de facto standard, and with good reason. Office is a very good productivity package that includes Word, Excel, and Powerpoint. Duke's site license makes the applications very affordable. When sending Word documents to others, it is wise to include versions of the document in some format other than Word. The PDF format renders documents quite well, and the Adobe Acrobat reader is free for people to download. It is also available for most operating systems, while Microsoft Office is not.
Lotus Notes & other email clients. The Duke Health Enterprise has standardized on Lotus Notes. Depending on the specific role you have in the system or the people you most frequently interact with, you may find Lotus Notes a good choice. However, many people have chosen not to use Lotus Notes, preferring instead to manage messaging and calendaring in other ways. The University technology group (OIT) recommends Mulberry as the email client.
The Notes application is set up by a system administrator.
Web browsers. The recommended web browser is Firefox which is a very useable and promptly updated application. It is open source software and is free to download. Unless a web-based application requires it, we ask people not to use Microsoft Internet Explorer. Some applications, most notably the Duke Health Enterprise's "eBrowser," require IE. Although it is necessary to update all operating systems and applications for security reasons, this has especially been the case for Internet Explorer. So, if you use it, be sure that it is the current version and that all patches have been applied.
Meetingmaker. For people who do not like Lotus Notes for calendaring, another product is available. Meetingmaker runs on Windows and Mac OS X platforms. The Meetingmaker server is operated by OIT.
Useful utilities. The following applications are site licensed for use by Duke students and staff (licensing details vary, however). They can extend the usefulness of Windows-based workstations.
- F-Secure allows Windows machines to log into and transfer files to Unix servers using SSH.
- WinZip is a compression and archiving utility.
- Micro X-Win32 allows Windows workstations to run Unix programs that use the "X window" graphical interface. Much bioinformatic and genome analysis software is available on the unix platform, and this program makes it possible to use it. For people who plan to do more than casual use of Unix-based software, we recommend using the Linux desktop or using a Macintosh running Mac OS X. Micro X-Win32 will only operate on machines located at Duke.
- TextPad is a "straight text" editor that accepts formats other than the standard "DOS" text formats.
- EndNote is bibliographic citation software that is well integrated with Microsoft Word