SEED/2012/Day 9

Searching the Primary Literature

Due April 14, 2012 (Day 9)

This assignment should take you about 15 minutes. The goal of this assignment is to teach you to search through the primary research literature and find papers that you want. You will need this skill in order to find information or key parts for your final design projects.

Primary research literature means peer-reviewed research papers published by the scientists who did the research (as opposed to scientific articles written by journalists, etc). You can sometimes find these papers on Google, but it is much quicker to use specialized search engines such as PubMed or Google Scholar. Scientific papers are peer-reviewed by other scientists before publication, and are published in journals like Nature, Science, and Cell (in biology). Unfortunately, most journals require you to have a subscription through a university before you can view the full text of their articles. (Some articles may have free full text, and others may not -- this is difficult to predict.) However, they will almost always let you view the abstract, a summary of the article, for free.

Instructions

Items 4, 5, and 6 will require brief (1-3 sentence) answers. You may write these down and turn them in at the beginning of Day 9, or email them to the instructors.

1. Visit Pubmed and Google Scholar. Try a few search queries and see what sort of results you get (search for topics related to your final project or anything else that interests you). On each search engine, find out how to narrow your search by Author of the paper, Journal in which the paper was published, and Date of publication.

2. Once you've got some search results, click through and look at some abstracts. (If you're using PubMed and you click on a search result, there will usually be a button in the upper right corner that you can click to view the paper on the journal's website.) Look for "Full text" or "PDF" links and try clicking those. Some papers will require a subscription, while others may be freely available.

If you find any papers that look relevant to your final projects, make a note of their citation information (title, author, journal, date) so you can find them again! To obtain the full text of papers that require subscriptions, you can visit the MIT library, or another university library. Or email the instructors, and we will use our subscriptions to get you a PDF.

3. Find the full text of this paper: (note: "et al" means "and the rest", i.e. the rest of the coauthors of the paper)

• Tabor et al. A synthetic genetic edge detection program. Cell. 2009 Jun 26.

4. Look at Figure 1 of the Tabor paper and read the caption. Summarize, in a few sentences, the point of Parts A-C of Figure 1 (you don't have to summarize part D).

5. What are the main sections of the Tabor paper? These should sound familiar to you from doing science projects or lab reports in school. (Note: the "Reaction-Diffusion Model" section is specific to this paper. Almost all papers have abstracts, but not many have one called "Reaction-Diffusion Model".)

6. Find the full text of this review article. Notice that it does not have any results or experimental methods, but instead focuses on summarizing other papers. How is the review article organized?

• Andrianantoandro et al. Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology. 16 May 2006.