2014-pre-workshop

Suggested Reading/Viewing before the Workshop

The parts directly relevant to the workshop are in bold.

Background Material

The workshop will give the participants hands-on experience in the cutting edge of biology and computational modeling of complex biological systems.  Modeling requires familiarity with concepts from numerous fields including Mathematics, Computer Science, and, naturally, Biology.  Unfortunately, relatively few professional scientists can claim to be equally proficient in all of these fields.  Our hope is that the workshop will inspire a new generation of scientists who will one day use modeling to solve some of the most challenging open problems in Biology. The following references are provided as background material.

Computer Tools

  • Switch 101: On Windows I used to...: We will have a room full of Macs, you will need to learn to navigate them. The user interface is actually what both PCs and Ubuntu have started to imitate, so it shouldn't be too awful if you haven't used them before.
  • Mac 101: Apple's introduction to Macs
  • Maple: We will use this to build and solve mathematical models of signalling pathways. You can get from the CUNY eMall. I can get it free, so I hope students can too.

Modeling

  • Executable cell biology, Fisher & Henzinger; Nature Biotechnology, 2007, 25(11) 1239-1249. This is a review of modeling techniques, if you are curious; it won't be directly used in the workshop.
  • BioNetGen Documentation: the main modeling tool that we will use. You will find the BioNetGen Primer the best place to start.

Biology

The main material that we will use in this section is the second bullet point, on Hallmarks of Cancer. The first bullet point is introductory information, which I hope will help to read the later material. The final bullet point is motivational material.

  • For a basic introduction, here are some wikipedia articles:
    • Cell Biology: The particular cell process that we will look at is cell signaling.
    • Cell Signaling: In particular, signalling pathways and the discussion of Figure 3. The discussion actually skips right past the crucial piece of the pathway for us, which is the Ras protein
    • Ras: This is a complicated protein that affects cell growth, and mutations of the Ras gene are implicated in lots of cancers. We will study its behavior in some detail.
    • Cell Cycle: It will be helpful to know the stages in the cell cycle. We will do an exercise on the transition from G2 to M in frogs.
  • Here is a current view of cancer that my research collaborators are particularly interested in. We will discuss this during the workshop.
  • The high-level motivation of the workshop is pancreatic cancer, but in basic research we dig into details rather than look at the big picture. Here's the big picture.

Notes on Reading Wikipedia articles

Several of the above links take you to wikipedia articles. You may be concerned about the credibility of these articles. If you are, it may be somewhat surprising to you that the quality of the technical articles tends to be quite good, especially in fields where there is neither political controversy nor strong economic interest.

Sometimes, you can get more feeling for the quality of a wikipedia article by clicking on the "Discussion" tab that appears at the top of the article. You will see that most of the above articles are part of larger efforts to systematize the information in major areas of knowledge such as "Molecular and Cellular Biology" and "Medicine".

Be a little slow to follow links, they can get you totally distracted; you might read through an article first to get the general sense, and then go back and follow links that look interesting or helpful.

Last modified: Dec 24, 2013