Welcome to CompBio! This page is aimed at getting new users up to speed and active in our research group as quickly as possible, by introducing our group conventions and philosophies, followed by a brief todo list. In depth treatment of these issues is available via the documentation sections from the main page which everyone should become familiar with.
[This is a document in progress. If seasoned CompBio members feel something essential is missing, feel free to add it. Similarly, if newbies feel like something needs to be better explained, start a section in here and others will fill it out.]
What does CompBio stand for?
CompBio is short for the Samudrala Computational Biology Group. The capitalisation and convention is exact since it refers specifically to our group, and not any computational biology group.
compbio in fixed width font is used when referring to it in virtuale, for example the domain name for computer hosts in our group is the prefix of
compbio suffixed to
washington.edu (which is top level domain name for hosts at the University of Washington).
Main article: CompBio philosophies
At its core, our group is about exploring science. Everyone in the group is a student of science and is dedicated to exploring life and how it works. All group members are given a lot of freedom to define their own projects and work on what they love. This is a group that is best described as "structured anarchy". Our group is much like nature itself, with order coming from entropy and no preconceived limitations in the way of achieving the most optimal results. Generally group members will work from home, collaborating with others with similar problems and projects. However, with great freedom, comes great responsibility. You are personally responsible for your project and the sooner you learn that, the more productive you will be. As such, this group rewards those who are self starters.
Main article: CompBio resources
These are a set of guidelines of things to be comfortable and familiar with. Although for most things, our group lets individual members do whatever they prefer, we have come to a consensus on certain things that keep the anarchy structured enough for work to get done.
We have our own mail server which handles all emails to and from compbio.washington.edu. Generally group email addresses such as email@example.com will be shorthanded as ram@compbio in the wiki. We have a variety of email lists, each of which has its own use:
agroup@compbio is our archived group email list. Anything that would be useful to have later on should go here including weekly reports but this is reserved mainly for science/research related discussions that pertain to the group. Please avoid sending trivial/noninformative emails to this mailing list.
pgroup@compbio is our unarchived email list sent out to all current group members, and is reserved for personal discussions that pertain to the group.
group@compbio sends out to all group members, past and present.
Generally, the majority of important group communication is through email. As such, make sure you check your email frequently, read through the emails all the way (they are quite information packed most of the time), and not be shy to voice any opinions / questions you have. Also, since we have a high volume of email in the group, please avoid attachments in your emails (attachments are a waste of space since they are replicated in every person's inbox and also increase Internet traffic and slow down loading time of mailboxes). Instead, upload to the CompBio archive and/or wiki and link to it in your email (if you don't have an archive directory, ask our current sysadm to create one for you). Also, there's no need to send emails that are just acknowledging receipt/reading/understanding of an email in a few words to every member of agroup (sending it to me is fine and I encourage that). Each group member is also expected to send in a Weekly Report over email to agroup@compbio by Wednesday night before our 2 pm group meeting on Thursdays in Rosen.
Our group generally uses linux for computing purposes. All our compute nodes and group shared computing systems run on linux, so if you are not familiar with linux, now is a good time to get started. There are a variety of good tutorials for basic terminal commands online which are a good place to start. For in depth documentation, always check the man page for a command (eg. man grep). However, the best way to learn this is really experience. If you are really dedicated to learning linux as quickly as possible, use it as much as possible. If you run into issues that take you more than 30 minutes to solve, do not be afraid to shoot out an email to the group for advice. We have probably all been there before and are more than happy to help.
Also, to prevent future head aches, please make extensive backups of your data. We have a lot of disk space between our machines and Network Attached Storage (NAS) devices, so there really isn't much excuse for not having several backups of your data. If you need advice on how to do this or want scripts to automate this, Google it and Read the Freaking Manual (RTFM) first. If you still are confused, send an email out to the group. Also, be sure to update your backups regularly. You should not lose more than a week's worth of work because of old backups.
To do for new members
Obtaining in virtuale access
The first and most important part of joining CompBio is obtaining in virtuale (i.e., virtual or computational) access to our computer systems/cluster. This will enable you to login to our cluster, send and receive email to other CompBio members and our mailing lists, and use and contribute to the wiki. This process should have initiated after your first meeting with us, followed up with an email confirming that you do want to join us. You then should've received an welcome introductory email confirming your account creation. If you do not receive this welcome email after joining us, please send an email to our friendly system administrator at
compbio with the full domain name.)
Logging to the CompBio cluster
Once you receive the welcome email confirming your addition to our cluster, you can login using Secure SHell (SSH) to connect to
abyss.compbio.washington.edu as per the computing instructions. Before you are allowed to connect to
abyss, you will need to send the IP address of the machines you are connecting from to our systems administrator so he can add it to our firewall. This needs to be done for any machine you wish to connect from. You can find out the IP address of your machine by typing in "what is my IP address" in Google and using one of the many tools provided.
Once you have logged into the
abyss, if it's your first time, please issue the
yppasswd command to change your default password (again, see the Documentation:Computing for more information). For the wiki account, simply login to CompBio and select your preferences on the navigation bar at the top right hand corner.
Obtaining physical access
Now that you can access our computer systems and do science, you need to get your own key and access card to the Rosen building. This is accomplished by filling out a building access and key request form. This is best done after our group meetings since you will need signatures and the person responsible for this task will help you filling the form out.
Although most members of the group do research from home, feel free to come in and use our resources at anytime.
Volunteer agreement and time sheets
If you are a volunteer, you also need to fill out the first page of our volunteer agreement. Also, at the beginning of each month you are encouraged to fill out a volunteer time sheet. These should be given to the responsible person (best done at our group meeting).