Welcome to Browser Staff

ID Cards

The GI admin office (E2 501) should have a preliminary building access card waiting for you when you start employment. To activate the card you will need to do the following:

• Have your photo taken at the Bay Tree Bookstore "ID Services" office (open M-F 8am-5pm). This is the photo that will appear on your access card.
• Have your card activated by Al McGuire in Baskin Engineering 399C (open M-F 1-3pm).

Once activated, this card will give you access to the E2 building and to several of the rooms on the E2 5th floor, including 515, 514, 505, the Intron Lounge, 599, and 510. If you have problems with access to any of these rooms, report them to Danielle or Lilia in the GI Admin office. You can also use this as a staff library card by taking it to the front desk at the Science Library or McHenry Library for a library barcode.

If activation of your photo ID key card is delayed for any reason, you can get a temporary ID key card from the GI Admin office that will give you temporary access to the building and offices.

You will also be issued a paper UCSC Staff card HR on your first day of work. If you take it to McHenry library, they will laminate it for you. Because our staff positions are funded by grants, your staff card may be replaced intermittently throughout the grant funding cycle.

Computer Accounts, Email and Google Apps

As part of your orientation, you will be assigned a ucsc.edu account. This account is typically used by UCSC to send you general announcements, payroll and HR information, etc.

Once your ucsc.edu account is set up, you will be able to set up an account with the School of Engineering (SOE) which may or may not have a different login name. You will receive an initial password for this account, which you should change during your initial login: https://accounts.soe.ucsc.edu/accounts/reset. This account will be used for SOE email and login access to machines and online resources.

For information about accessing your SOE email, see: http://support.soe.ucsc.edu/e-mail.

• The default email configuration uses the SOE gmail server accessed from an email client such as Thunderbird, Outlook or directly from gmail. For more information click the 'web e-mail home page' link in the 'BSOE Web-Based E-Mail' section of the SOE email support page listed above.
• To eliminate the need to check your slugmail (UCSC) account on a regular basis, you can automatically forward the messages to your SOE account. Set up forwarding through the Settings menu on your gmail client.

Once your SOE account has been set up, email 'cluster-admin@soe.ucsc.edu' to request your GI computer account (include your supervisory manager's name). This will give you access to several machines used by our group. Be sure to ask for them to add you to the UNIX groups: genecats, and protein.

If you have problems with GI software, hardware, or accounts, send email to the systems administrators (cluster-admin@soe.ucsc.edu). If they can't handle your question, they'll refer you to the appropriate person. The SOE admins use the ITS ticketing system: ITRequest: http://its.ucsc.edu/get-help/itr.html

In addition to your email account, UCSC will also provide you with a CruzID account for accessing campus web resources, such as your timesheets, benefits information, etc. There are two kinds of CruzID accounts: Blue and Gold. You can set up or change the passwords for these accounts here. This page also contains a FAQ.

You will be expected to keep your Google Calendar up-to-date with your work meetings and your days off. You must use the Google Calendar associated with your @ucsc.edu email address (not your @soe.ucsc.edu address). Read more here for background and details: Google_Calendar. Once you get your own calendar set up, you may want to add the following calendars to yours using these ical urls:

• Genecats: http://www.google.com/calendar/ical/soe.ucsc.edu_maj8uamno3vkkfint5t8ll56n8%40group.calendar.google.com/public/basic.ics
• Genome Browser Mail List: http://www.google.com/calendar/ical/soe.ucsc.edu_54vch7pcqotonm64f25nl65ub0%40group.calendar.google.com/public/basic.ics
• Release Schedule: http://www.google.com/calendar/ical/soe.ucsc.edu_r3m0u3g5o4glfer53i9vbe596s%40group.calendar.google.com/public/basic.ics

For more information on Google apps provided by SOE see: http://support.soe.ucsc.edu/google-apps.

Parking, Busses, & Vanpools

Parking permits, Metro bus passes, and other campus parking and transportation options are handled through Transportation and Parking Services (TAPS). The TAPS office is at the base of campus, just north of the Bay & High entrance.

There are several on-campus parking options available carrying a wide range of costs. Carpool and scratch-off permits are an economical alternative to "A" permits. The TAPS parking permit page describes each of the parking permit options and provides a link to the online parking permit application.

There are two kinds of bus service on campus: campus shuttles and Santa Cruz Metro buses. Campus shuttles, which are internal to campus, are free and do not require an ID to ride. The various routes and schedules are described here. To ride the Metro bus, you must purchase a staff bus pass or pay a fare. See the TAPS bus page for information about Metro bus passes, routes, and schedules.

If you live outside of Santa Cruz, you might be interested in joining a vanpool.

The campus also offers a bike shuttle from town, and a zipcar program.

Printing, Copying & Wireless

NOTE: In 2022 3/28 we moved off IT support so the below may no longer apply.

Instructions for configuring your computer to print: https://support.soe.ucsc.edu/printing

In a nutshell for Mac go to Sys.Prefs. and Click IP to add "papercut.soe.ucsc.edu:631" and in queue add "printers/midnight". That printers/printerName is located at http://papercut.soe.ucsc.edu:631/printers/

Put in address (no space): "papercut.soe.ucsc.edu:631"
Have Protocol: IPP
Put in queue:  printers/midnight
Put in name: midnight
Put in location: Room XYZ
Use: Generic PostScript Printer
Click Add. 

Printers available for our use:

• "lollipop" -- color ink printer
• "midnight" -- black ink printer

To set up wireless on your laptop, see: http://its.ucsc.edu/wireless/eduroam-security-cert.html (For a mobile Apple device you need to open a link in Safari).

Note: The printer set up may be different depending on our OSX (Sierra), you may need to follow these steps where you add a line like smb://ad-winprint.ad.soe.ucsc.edu/coffee

Office Supplies

General office supplies are located in the small cabinet in the corner of room 515. You can take what you need from there. You can order anything else you need from through the staff in the GI Admin office.

Telephone & Ethernet

There are shared phones in the GI office spaces, almost no one has a desk phone. Ask your officemates about the sharing policy and protocols. If you need your own phone, talk to your supervisor. Campus phones share the 459 prefix (area code 831). When dialing from campus phone to another campus phone 459-XXXX, just dial '9XXXX'. To call off-campus from campus phones, prefix with '6'. To move phones, for example if a cubicle changes locations, according to the student workers it should work to make a facilities request, facilities-request@rt.soe.ucsc.edu, to move phone at port 5321 to port 4321.

For an ethernet cable connection to your desk you can create a ticket in the campus ticketing system by emailing ucsc@service-now.com. All IT services requests (i.e., activating data ports, etc) can be sent to ucsc@service-now.com. However, be sure to specify SOE somewhere in the subject line too to help get it into the proper queue. If you are getting no response you can copy Lynne Sheehan at sheehan@soe.ucsc.edu.

Getting Paid

Timesheets are submitted online via CruzPay: http://cruzpay.ucsc.edu/. You will need a CruzID Blue login to access CruzPay. If you have questions about filling out or submitting your timesheet, consult the CruzPay help pages or ask your supervisor.

Timesheet and paycheck schedules differ, depending on your position:

• Non-exempt staff (P/A2 positions): You submit a timesheet biweekly and are paid biweekly. The payroll deadlines and paydates are listed here; the timesheet due date is also shown on your online timesheet form.
• Exempt staff (P/A3 and P/A4 positions): You submit a timesheet at the end of every month, and are paid on or around the first day of every month.

If you want your paycheck to be deposited directly into your bank account, follow the instructions here. You will need an "At Your Service Online" (AYSO) login to access this information. The page will help you set one up if you don't already have one.

Your pay statements are available online here. (AYSO login required)

For complete information on payroll options, direct deposit, earnings statements, etc. see the Financial Affairs website.

Our Location

Mailing Address:

Mail Stop: Genomics Institute
University of California Santa Cruz
1156 High Street
Santa Cruz, CA 95064

FAX Number: 831-459-1809

Mailing Lists

A caveat for subscribing to the mailing lists: DO NOT use your regular login password as your mailing list password. Be sure to provide the email address that you plan to use for posting messages to the mailing list - posting from any another address will be unsuccessful.

Sign yourself up for these mail lists:

• School of Engineering (SoE) Staff mailing list: http://groups.google.com/a/soe.ucsc.edu/group/staff?hl=en
• Browser-staff: http://groups.google.com/a/soe.ucsc.edu/group/browser-staff?hl=en
• Genecats: http://groups.google.com/a/soe.ucsc.edu/group/genecats?hl=en

Ask your project manager to add your email address to project-specific mailing lists.

These are the external Mail Lists (where Genome Browser users write to ask questions). You can join them when you are ready:

• genome mailing (UCSC genome browser discussion) list: https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome
• genome-mirror mailing (UCSC genome browser mirror discussion) https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-mirror
• genome-announce mailing (UCSC genome browser announcements) https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome-announce

Wiki Sites

We have two wiki sites:

• the external wiki which is our public wiki. You can sign up for a login to get editing privileges. http://genomewiki.ucsc.edu/index.php/Main_Page
• the internal wiki (a.k.a. genecats wiki) (this one!). You will need to request a login from Hiram or BrianL to make edits (it's already public, so if you're reading this without a login, you'll still want one for the day you'll be updating pages) http://genomewiki.ucsc.edu/genecats/index.php/Main_Page

Tutorials

• A list of other training resources.
• A review of current Genome Browsers (2019): http://tinyurl.com/genome-browsers

Tools

• Vi
  • Don't have a text editor of choice? Learn how to use vi by typing in "vimtutor" on the command line on hgwdev.
  • Vi Quick Start Guide
  • Handy Cheat Sheet

• UNIX Commands
• MySQL Commands
• Common Scripts
• Never edited a wiki page before? Here's a wiki cheat sheet!

Redmine

Redmine is our project management and bug-tracking software. Ask Ann Zweig for a login and tutorial.

Additional Orientation Info

• See the Getting Started on the Genome Browser Project Team for additional (slightly outdated) information
• See the QA Home Page for more info on the QA process.
• See Popular Links

Useful Links

• UCSC Genome Browser: http://genome.ucsc.edu
• Genome Browser FAQs: http://genome.ucsc.edu/FAQ
• Browser Staff internal wiki: http://genomewiki.ucsc.edu/genecats/index.php/
• Genome Browser public wiki: http://genomewiki.cse.ucsc.edu/index.php/Main_Page
• Redmine project tracking: http://redmine.soe.ucsc.edu/
• Genome Browser push queue: http://hgwbeta.cse.ucsc.edu/cgi-bin/qaPushQ
• QA wiki: http://genomewiki.ucsc.edu/genecats/index.php/QA_Home_Page
• UCSC campus maps: http://maps.ucsc.edu/
• UCSC A-Z websites: http://www.ucsc.edu/about/alpha_index.asp
• UCSC directory: http://www.ucsc.edu/about/find_people.asp
• Genomics Institute home page: https://genomics.soe.ucsc.edu/
• SOE IT computer support information: http://support.soe.ucsc.edu/
• Selected publications by the UCSC Genome Bioinformatics group and collaborators: http://genome.cse.ucsc.edu/goldenPath/pubs.html
• Presentations given by Browser Staff both internally and at external meetings: http://genomewiki.ucsc.edu/index.php/Presentations

Learning about the Genome Browser

• Familiarize yourself with the Genome Browser, Table Browser, BLAT and other tools: http://genome.ucsc.edu/
• Genome Browser User's Guide: http://genome.cse.ucsc.edu/goldenPath/help/hgTracksHelp.html
• OpenHelix Training Materials: http://www.openhelix.com/downloads/ucsc/ucsc_home.shtml
• Jim's initial paper on BLAT: http://www.genome.org/cgi/content/abstract/12/4/656
• Check out this 2019 paper reviewing multiple Genome Browsers.

For QA Staff

• Places for QA to start (in addition to this page):
  • QA Home Page
  • Browser QA Training Category

• Ask Ann to add your email address to the following alias lists:
  • browser-qa
  • qa-only (this is for use in redmine)
  • push-request
  • genome-www