Welcome

WELCOME TO THE SYSTEMS BIOLOGY LAB

First of all, don't panic. There is a lot of new information and a lot to learn, but no one expects you to absorb everything at once. If you don't know, don't remember or you're unsure how to do something, just ask anyone at the lab.

GENERAL ADMINISTRATIVE INFORMATION

Contact info for admin matters:
The lab's project coordinator: Jenni Lahtinen (jenni.j.lahtinen at helsinki.fi)
The lab's EU coordinator Ann-Christin Ostwaldt (ann-christin.ostwaldt at helsinki.fi)
The Research Program Unit's (RPU) secretary: Maaria Puupponen (maaria.puupponen at helsinki.fi), Anne Simola (anne.simola@helsinki.fi)
ONCOSYS program coordinator: Karen Ahlnäs (karen.ahlnas at helsinki.fi)
The HR coordinator: Päivi Sinisalo (paivi.sinisalo@helsinki.fi, hr-ltdk@helsinki.fi)

In tax card, employment contract and grant agreement issues and for almost anything else, you can and should contact Jenni. For information on how to get a tax card see the links below.

Check list for all new employees for the first day(s):

• Keys:  
  You need a key card to get into the building and to the lab. Contact Jenni for the key application. With the key card application form and an ID you'll need to go the security center (just outside of Biomedicum) to have your photograph taken.
  After a day or two you can pick up the key card form the key office on the 2nd floor of Biomedicum next to the main elevators (open Mon, Wed and Fri from 13 to 14.30).
  When picking up the key card, ask for a pin code; you'll need it to get into the building before 7.30, after 19.30 and in the weekends. 
  If your contract is for less than 3 months, you'll get a flexim key instead of the key card, in that case you can go straight to the key office with the application form, no photograph needed.
  Remember to return all keys when your contract or agreement ends.

• Biomedicum Helsinki intra   
  The RPU secretary will add your information into the Biomedicum Helsinki intra, this is a requirement for you to get the pin code for the card.
  From the intra you can also find the contact information for everyone working in the building.

• IT user account  
  Fill in the IT user account application form, sign and send it to helpdesk@helsinki.fi. You will receive an email (to the email address you've given) when the account has been created and instructions on how to activate it. If you have Finnish internet banking codes, you can activate the account using those, if not, you'll need to visit the ID point in the Terkko library (next to Biomedicum) first with a valid ID. Note: video ID during corona restrictions.
  If you already have a University of Helsinki email address and user account from another unit, ask the HR coordinator to transfer those under the Research Programs Unit, unless you're still an undergraduate student.

• Staff ID card  
  In order to receive personnel discount for lunch at the UniCafe or Ravioli cafeteria, or at Unisport, you'll need a staff ID card (used to be included in the key cards, but now requires a separate card). In order to be eligible for the card, you'll need to have a minimum of 4 month employment contract to the University (grant receivers are not eligible). If your contract is for less than 4 months, you can get a temporary card from the human resources coordinator (Maria). See the links below for instructions and the form for ordering the staff card.

• E-mail list  
  Each group has a mailing list, give Jenni and the RPU secretaries your email address (usually your helsinki.fi address, but you can use something else too) to add on the list. All lab info and general notifications concerning Biomedicum are sent to this list.

• Telephone & telephone directory  
  There is a phone in the lab (02941 25407 or 050 4486327, or just 25407 from other university numbers) that can be used for work related calls. Also Jenni's work phone can be used for calls.
  The RPU secretary sends updates to the telephone directory every few months, but you can also have yourself listed or update your info by sending your name, title (PhD student, postdoc etc), work phone number (above), unit and address (see below: where you work) to the university phone services (puhelinvaihde at helsinki.fi). If you're only staying for a short period, this won't be necessary.

• Changing rooms & lockers  
  There are changing rooms and showers at the P-floor of Biomedicum that you can access with your key card / flexim. If you're biking or running to work on a regular basis and need a personal locker, ask Jenni about the key.

• Parking  
  Parking space is quite limited on the Meilahti campus, to ask about parking permits and prices contact Satu Sankkila (satu.sankkila at helsinki.fi, room A405b).

• Printing 
  You can print to any of the shared Canon smartcard printer-scanner-copy machines (there's in the entrance to the ONCOSYS space) from a university registered computer by choosing any Smartcard printer and then logging into any of the multi-function printers  with your key card or staff ID card.
  If you're an undergraduate or visiting student at the University of Helsinki with limited printing rights, you can ask the Meilahti service coordinators (ltdk-palvkoord at helsinki.fi) to give you staff printing rights for the duration of your grant agreement / visit.

• Common/Shared hard drives
  All data are kept on file servers shared across our computing infrastructure. We host our own download / upload services to collaborators.

Other relevant information

• Working hours, holidays and sick days (for those with employment contracts, doesn't apply to grants)
  Research and teaching staff (including PhD students and postdocs) are expected to work 1624 hours / year (from August to July), and with the average of 7 h 21 min (+ lunch) in a working day that leaves about 6 weeks of time off per year. You should agree on the holiday dates with your supervisor and add your holiday to the lab holidays excel sheet. Those with an employment contract (not grant agreement)  must notify all holidays and sick days to the SAP Fiori Work Time Allocation system that is used to allocate working hours to projects. The lab's coordinator sends a reminder of these every month. 
  You can take up to 3 sick days in a row without a doctor's certificate. For longer absences you can send your doctor's notice to palkka at helsinki.fi. Having a sick day on Friday and the following Monday counts as 4 sick days, even if you were not sick during the weekend. Remember to notify your supervisor immediately when you have to take a sick day.  
• Occupational health services (for those with employment contracts, doesn't apply to grants)
  Those with an employment contract can use the University of Helsinki Occupational Health Services at Mehiläinen medical center during weekdays between 8.00 and 20.00. Primarily all appointments should be made to the occupational health doctor in charge of the Faculty of Medicine personnel, but in case of acute illness you can be referred to any available general doctor. Remember to mention that you are an employee of the University of Helsinki when you make the appointment. The most convenient way to make an appointment is trough the Mehiläinen app. See Flamma for more detailed information.
  In case of acute illness at other times, contact the public health services (advice 24h / day from number 09 3101 0023 ). If you do not have a Finnish social security card (Kela card), then an additional health insurance is recommended to avoid excess costs in case of accidents or serious illness etc.
  If you have a grant agreement instead of an employment contract, then you cannot use the University's occupational health services. Make sure to take the MELA insurance for yourself if you are on a grant.        

• Safety information
  Please read the the University's safety guide (hard copy in the lab, pdf in Flamma). At the very least, make sure you know the location of the nearest first aid cabinet, emergency exits (near the toilets) and fire extinguisher (near the kitchens on each floor and wing). In case of fire alarm, always leave the building using the emergency exits, not the main stairs or lifts.

• Unisport
  There are university gyms and sports facilities on all the campuses with a wide variety of classes and courses. University of Helsinki personnel (which does not include grant receivers) and students have a discount for the sports fees at Unisport.

If you're just moving to Helsinki:

• Registration at the local register office (maistraatti) 
  If you're just moving to Helsinki (and staying for more than 3 months), you'll need to make a notification of move to the Local Register Office (maistraatti). For foreigners, contact the University International Staff Services (link below) for information and help on other immigration formalities.

• Travel card    
  To use the public transportation in the Helsinki area (also Espoo and Vantaa), you can get a personal travel card, where you can either upload time or value or download the HLS mobile app (or Whim mobile app). In order to get the resident price, you must first register at the local register office (see above). You can get the card from the HSL service point under the main railway station and upload time / value at any R-kioski or ticket machines at the train and metro stations. More info about the card, ticket prices and finding your way around in Helsinki, see below the link Public transportation in Helsinki.

• Phone
  If you don't have a Finnish phone number yet, the easiest way at the beginning is probably to get a prepaid sim-card from R-kioski (there's one across the street from Biomedicum). Operators for phone and internet services include Saunalahti, Elisa, Sonera, DNA, etc.

LAB SPECIFIC INFORMATION

Check list for new lab members on the first day(s):

• Public profile. Send your information, short description of your work and a portrait photo of yourself to Jenni.
• Make a wiki page about yourself at the LAB Member pages. Include at least: Full name, contact info, your office hours and list of projects.
• Join the lab telegram channel (anyone from the lab can send you the invitation linke) and the ONCOSYS slack (ask Karen for the link)
• Ask someone in the lab to add you to the lab google calendar
• Ask for a walk through of your laptop environment from our IT support (once you have activated the user account). We use the university maintained version of Ubuntu Linux, named Cubbli. Our lab has a range of tools pre-installed to help in your daily routines.

Things you should know

• Where you work 
  The Systems Biology of Drug Resistance in Cancer Lab, also known as the Hautaniemi lab, belongs to the System Oncology (ONCOSYS), one of the 9 programs that form the Research Programs Unit (RPU), in the Faculty of Medicine. This is your main affiliation. The lab is also affiliated to the Department of Biochemisty and Developmental biology in Medicum, also part of the Faculty of Medicine. Both affiliations should be mentioned in any publications etc. 
  The lab is located on the 3rd floor of Biomedicum Helsinki 1, room B317b. 
  Your work address for receiving mail is Hautaniemi lab, Haartmaninkatu 8 (POB 63), 00014 University of Helsinki, and visiting address Haartmaninkatu 8, 00290 Helsinki.
• The boss    
  Sampsa is Professor of Systems Biology in Medicum, however, you can just call him Sampsa instead of Prof Hautaniemi. He has no specific hours for meeting students etc., so if you need to talk to him, just knock on his door whenever he's not having a meeting or on the phone. He also answers emails quite frequently.

• Group meetings and other lab events
  Group meetings are once a week (currently on Wednesdays at 13), and the schedule is in Wiki and the lab google calendar. Everyone should attend these.
  Other regular lab events include the Coding Camp in June (a two-day work retreat usually in Nuuksio), and Christmas dinner in December, usually preceded by ice skating or some other activity.  All lab events are marked to a google calendar, ask someone at the lab to share the calendar to you.   
• Communication
  - Lab external website (see the links below) is updated by Jenni, send her your profile info    
  - Lab mailing list (grp-hautaniemi) is also updated by Jenni, give her the email address where you want to receive work related mails.
  - Lab wiki pages: A place to store our practical knowledge. Read and edit regularly!
  - Slack: A chat protocol to reach other lab members when not at the lab, more info in our Lab wiki
• Lunch    
  There are two cafeterias near by, Ravioli in Biomedicum and UniCafe across the street at the Haartman institute, both have discounts for University personnel (with the staff ID card) and undergraduate students (with a Finnish student card). There is also a small kitchen on every floor and wing with a fridge and a microwave oven, if you prefer to bring your own lunch.   

What's expected of you:

• If you're a BSc / MSc student  (ToDo)
• If you're a PhD student
  In order to conduct PhD studies, first you'll need to apply for a right to pursue a doctoral degree at the Faculty of Medicine. See the links below for information on how to apply. You'll need to choose a Doctoral Program, which have some funded positions; you should also apply for these, see below links for relevant Doctoral Programs.

• If you're a postdoc  (ToDo)

Lab dictionary

• Anduril: Software developed by the lab to analyse data
• Component: Separate program that runs a small piece of an analysis
• Pipeline: Collection of steps of analysis (components), sent to Anduril to run.
• Mercurial: Version control system we use.
• Bitbucket: Online service providing us version control and bug hunting ticket system.
• CSC: IT center for science - is where our processing happens
• VM: Virtual Machine - Computer safe to experiment on and crash
• Cloud/Cluster: Collection of several cooperating VMs
• Telegram: Chat, our way of discussing daily matters from afar
• More detailed dictionary

Useful external links:

• • Lab external website
  • Genome-Scale Biology Research Program
  • Anduril glossary
  • International staff services 
  • Unisport
  • Local Register Office (Maistraatti)
  • Tax card
  • Public transportation in the Helsinki area
  • Faculty of Medicine (how to apply for a right to pursue doctoral degree)
  • Doctoral Program in Biomedicine (DPBM)
  • Integrated Life Science Doctoral Program (ILS)

Links to internal pages (after you have the Helsinki university user account):

• LAB Read Me (on lab wiki pages: further information on working in the lab, running analyses, best practices etc.)
• LAB Administrative Info (on lab wiki pages: includes more information on salaries / grants, working hours and absences, work travel, office supplies etc.)
• LAB Member pages (on lab wiki pages: contact and holiday info on all lab members)
• Biomedicum Helsinki intra (contact info on everyone in the house, Ravioli lunch menu, events calendar, maintenance requests)
• Flamma (University of Helsinki intra, logging in to SAP HR)
• Staff ID card (in Flamma)
• SAP Fiori