Starting in David's group

• An older, non-wiki version of this page is on [1]
• You might want to print this page

Before leaving

• Visa at home: J-1 visas have high priority, you get them often one day after the embassy appointment. But don't underestimate the time it takes to get an appointment and all the paperwork. You need to pay a fee for the SEVIS website (=the database of foreign students/scholars), a fee for the embassy and a fee for the appointment. Keep the SEVIS receipt PDF, you'll need it every year afterwards during your postdoc. The appointment itself takes only a few minutes, plus some waiting time. The embassies are actually very well organized, so while they make a big fuss of every little detail in the application forms, in Munich at least you can show up without a picture (there is a machine), without the stamps (machine), with a mobile phone (they keep it) and even without the application printout (they have PCs and printers). In Paris it's a bit different, you absolutely need most of the paperwork and the visa fee receipt, as you cannot get into the building otherwise.
• Don't bring too much stuff. Everything is cheap here on craigslist. Bikes, etc are easy to find especially at the end of the University term. Moving companies are very expensive and it will take them 2-3 months to get your stuff across any ocean, even if they say otherwise (once they have your boxes, they don't care anymore).

For aliens in Santa Cruz

• • For general advice on how to start in the US and in Santa Cruz in particular, see Jill Bejerano's old page, tons of interesting stuff, unfortunately, not all of this is valid anymore (e.g. credit history is becoming less important)
  • Count on running around for 2-3 weeks to get all the paperwork done
  • J1 Visa: No rush, you have at least 10 days. You need ISSS to get your SEVIS entry OKed before you can apply for a social security number. After this, you have to wait until a time that is at least 10 days after your entry into the US, and 48 hours after ISSS has made the entry. You need to bring your DS2019 to ISSS and your passport with the I94 inside. At the social security office, you can shorten the wait by filling out a "new SSN" forms next to the entrance, on the wall. If you show up at 9:15, then the waiting time is usually not longer than 10 minutes. Show up at 11:00 and you might wait for an hour.
  • You can get the SSN two days later by going to US Soc Sec Adm again
  • You can have the social security card sent to the lab, just make sure that you have the right address, with the "Mailstop: CBSE-ITI" mentioned on it.
  • Next step: Open a bank account
    • For foreigners: Rather avoid credit unions and local banks: They are difficult to wire money to as often they don't have SWIFT BICs
    • Bank of the West insisted on a proof of address, Bank of America, Chase, Wells Fargo, etc seem to be easier
    • My recommendation: Go to BoA, Wells Fargo or Chase, so you can transfer money from abroad
    • If
    • Don't believe what the banks tell you: You can open an account without a social security number. Sometimes they will restrict the account (no debit, no checks). In this case, you can go to a different bank
    • Wells Fargo didn't have any restriction on non-SSN accounts
  • Send the SSN to HR (Jolinda) and the bank account details to leeann@ucsc.edu
  • As an alien (not Canada), you don't need to pay tax for two years: http://www.ucop.edu/ucophome/cao/paycoord/taxstate.html
  • Depending on the Tax Treaty, you might have to reimburse taxes if you stay more than 2 years and 1 day (England) (not France, Germany, Spain)

Santa Cruz

• Map with places we like, eating places, supermarkets, bars, etc [2] , created by Thomas Juettemann and Max

Administrative

• Postdoc office phone numer: +1 831 459 5232
• Address
  • Mail Stop: CBSE/ITI
  • Mailing Address: 501 Engineering 2 Building, Mailstop CBSE/ITI, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064
  • FAX Number: 831-459-1809
• You will have an appointment at Human Resources on the ground floor of the Engineering 2 building (=our building) where you will have to fill out and sign tons of forms. They also give you a campus map
• Healthcare:
  • Medical: Do some research on the difference between PPO and HMO on Wikipedia. PPO means that you pay per service, but you can select and change doctors at your will, you can see specialists. With HMO you have to go to an assigned family doctor who might not be what you want and you cannot see specialists without his approval. The details are buried in PDF files here and you can also look up the available doctors in the Santa Cruz area for each plan.
  • Do *not* take the Dental HMO plan! The PPO plan costs you the same and you will be able to choose your dentist! The HMO dentists are at Watsonville, San Jose and Los Gatos, impossible to reach without a car, and you cannot choose one yourself, if you don't like your assigned dentist.
• Use the map to get to the University ID office, they will print your ID card (it is located at the intersection of Steinhart / Hager roads) see also campus map http://interactivemap.ucsc.edu/
• Go to see Al McGuire in the Baskin Engineering building (the old building just in front) in room 399 amcguire@soe.ucsc.edu, open from 1pm to 3pm, to get your card activated. Take the bridge, go upstairs one floor, it's in the big floor that crosses the whole building, on the right hand side when looking from Engineering 2
• If you plant to cycle to work, ask him for a key to the showers (Eng, ground floor, next to bathrooms)
• Once HR has entered your SSN into their system, one day later, you will be able to use the ucop website "atyourservice [3]
  • You CAN apply for a direct salary transfer here, even though HR won't believe it, do this immediately, otherwise you will get a check with your salary.
    • You can cash them in for free at Wells-Fargo, they will very very aggressively try to sign you up for a bank account. Don't believe them that you need to sign up for them to cash in the check, they supposedly have an agreement with the University to do it for free (and try to get new bank customers via that route). On the other hand, Wells Fargo is one of the better-organized banks and has decent service.
    • Bank accounts: Be aware that transfers from abroad onto Union (Bay Area or Community Credit Unions) are quite difficult as they don't have Swift/BIC codes.
  • You need to enter your SSN without hyphens and your birthdate as mmddyy when you create your login
  • Sign up immediately for the health plan, you have only 30 days to do this and you can do it via ucop
  • Make sure that your address in ucop is correct: The health company will send you insurance card to it
• You should have an SOE account / SOE email address, this should have been done automatically via the CBSE admin office
• You will receive cruzID registration emails
  • define your passwords
  • redirect your cruzId emails to your SOE account
• Order office supplies from gopalace.com, copy shopping cart into email and send to Danielle
• Note the intranet webpage of CBSE, it allows you to books rooms and download reimbursement forms.

Travel

• Get travel insurance for free from http://www.ucop.edu/riskmgt/uctrips/
• Get travel reimbursement forms from https://cbse.soe.ucsc.edu/travel
• The UCSC pretrip guide is actually not that bad: https://financial.ucsc.edu/Pages/Travel_PreTripGuide.aspx#before

Meetings and groups

• Subscribe to any of these mailing lists (genecats and staff is recommended, other depending on your preferences)
  • genecats: https://lists.soe.ucsc.edu/mailman/listinfo/genecats
  • Staff: https://lists.soe.ucsc.edu/mailman/listinfo/staff
  • Genome reconstruction aka "David group meeting": http://lists.bx.psu.edu/options/rec
  • Haussler Wetlab aka "Salama group meeting" https://lists.soe.ucsc.edu/mailman/listinfo/hausslerwetlab
  • Cancer group: https://lists.ucsc.edu/mailman/listinfo/cancercats
  • CompBio (PSB compbio news+Kevin's son's theatre performances) https://lists.soe.ucsc.edu/mailman/listinfo/compbio
• Other email lists here are aliases on the SOE mail system, /var/mail/aliases on the moondance machine, email bob kuhn to subscribe
  • browser-qa
  • browser-staff aka "Kent group meeting"
  • cluster-staff
  • encode
  • genome-www
  • push-request
  • these two are managed by the CBSE admin office and you should be subscribed automatically:
  • hausslergrads
  • hausslerwetlab
• If you work on the browser sourccode, sign up for a redmine account, email Ann Zweig for details. Redmine is the bug tracker used here for internal browser communication
• If you want to modify the browser source code, you need to pass the "git test", be added to the git group and need a pushqueue account, search for git on this wiki and learn how to modify a source file, then talk to Galt to pass your text
• There are the following meetings during the week and their MCs:
  • Monday: Browser Staff Group 11 am (Ann Zweig)
  • Tuesday: Immuno Journal Club 11 am (Ngan and Hyunsung)
  • Wednesday: Wetlab 12:30 (Salama), Genecats 2 pm (Donna), Cancer Group 3:30 pm (Jing)
  • Thursday: Recon Group (Benedict/Dent), changing schedule
  • Friday: Nothing?

Technical

• Closest scanner: Front office, second door on the right, just enter your email and press scan
• Out-of-hours Scanner: Get copy card in postdoc room (Daniel's cube?), 2nd floor, media room, enter card, press "scan", enter email address of recipient, press copy button
• Printer: Add the "oops" printer (yes this is the DNS name), select the IPP protocol if asked
  • Color printer is in the front office, HP Color LaserJet CP4520 Series, hostname "lollipop"
  • Other printers: http://support.soe.ucsc.edu/printing
• Fax: Ask at front desk or see scanner
• Reserve a room: https://cbse.soe.ucsc.edu/conf/reserve/form

• Clusters
  • swarm : ~ 200 nodes, 4 CPUs each 8GB RAM
  • encodek : 5 nodes, 4 CPUs each, 16GB RAM
  • memk : 8 nodes, 2 CPUs each, 32 GB RAM

• Account config
  • use /cluster/install/utilities/chsh to change your shell to bash
  • copy ~hiram/.bashrc.hiram to your homedir and add the line "source .bashrc.hiram" to your own .bashrc file
  • Never put anything into your homedir when working on the cluster, create a new data store dir on /hive/users/<youname>
  • If you have any problems with your account, email cluster-admin@soe.ucsc.edu
  • Read Cluster Jobs and "Where is everything" and "Parasol Manual"
  • make sure that you are a member of the "genecats" and "protein" groups
  • You might want to add this statement as well to your bashrc, will add tab completion to the para command:

 complete -o default -W "create push try shove make check stop chill finished hung slow crashed failed status problems running hippos time recover priority maxJob resetCounts freeBatch showSickNodes clearSickNodes" para

• Cancer stuff:
  • Install http://openvpn.net/index.php/open-source/downloads.html if you're on Windows or Mac
  • Get the .key and .cert files from Erich and place them into the openvpn/config directory.
  • place the .ovpn file into the same directory, adapt the paths
  • open the ovpn file with openvpn

Genome Browser

• • Email cluster-admin and ask them to setup your own browser
  • check out the kent source tree via git into /hive/users/<yourname>/kent and run make in lib, hg/lib and then "make cgi"
  • create a hg.conf in /usr/local/apache/cgi-bin-<yourname>/ copy an existing one from e.g. /usr/local/apache/cgi-bin-pauline
  • modify the line with db.trackDb to read db.trackDb=trackDb,trackDb_<yourname>
  • modify your ~/.hg.conf: add username and password (ask someone else, anyone who has set up their own browser, to give you the write-access password for hgwdev's mysql), modify the line db.trackDb to point to trackDb_<yourname>, like this: db.trackDb=trackDb_<yourname>
  • create a new trackDb directory structure in your homedir, something like ~haeussle/usr/trackDb
  • add a new track to hg19 trackdb, run "make human" to show the track and check on <yourname>.cse.ucsc.edu http://hgwdev-<yourname>.cse.ucsc.edu that everything works.