CSB Assignment Week 1

Assignments for Week 1

Note! This assignment is currently active. All significant changes will be announced on the mailing list.

 
 

Exercises for this week relate to this week's lecture.
Pre-reading for this week will prepare next week's lecture.
Exercises and pre-reading will be topics on next week's quiz.

Reading from last class

Two papers that discuss the concept of system in systems biology. This is intended as brief reading, to reinforce some of the ideas we explored in class. You should be familiar with the main concepts that are discussed here, but I will not require you to reproduce details of the articles in the quiz.

Bizzarri et al. (2013) Theoretical aspects of Systems Biology. Prog Biophys Mol Biol 112:33-43. (pmid: 23562476)

[ PubMed ] [ DOI ] The natural world consists of hierarchical levels of complexity that range from subatomic particles and molecules to ecosystems and beyond. This implies that, in order to explain the features and behavior of a whole system, a theory might be required that would operate at the corresponding hierarchical level, i.e. where self-organization processes take place. In the past, biological research has focused on questions that could be answered by a reductionist program of genetics. The organism (and its development) was considered an epiphenomenona of its genes. However, a profound rethinking of the biological paradigm is now underway and it is likely that such a process will lead to a conceptual revolution emerging from the ashes of reductionism. This revolution implies the search for general principles on which a cogent theory of biology might rely. Because much of the logic of living systems is located at higher levels, it is imperative to focus on them. Indeed, both evolution and physiology work on these levels. Thus, by no means Systems Biology could be considered a 'simple' 'gradual' extension of Molecular Biology.

Westerhoff (2011) Systems biology left and right. Meth Enzymol 500:3-11. (pmid: 21943889)

[ PubMed ] [ DOI ] Systems biology has come of age. In most scientifically active countries, significant research programs are funded. Various scientific journals, standards, repositories, and Web sites are devoted to the topic. Systems biology has spun off new subdisciplines such as synthetic biology and systems medicine. There are training courses at the M.Sc. and Ph.D. level at various Universities. And various industries are engaging systems biology in their R&D. Systems biology has also developed numerous new methodologies. This chapter attempts to organize these methodologies from the perspectives of the unique aims of systems biology, and by comparing with one of its parents, molecular biology.

Student Wiki

If you have taken BCH441, you have already done this task. Please take a moment however to add a category tag to your page

[[Category:BCB420_2014]] or [[Category:JTB2020_2014]].

Collaboration is a common theme for modern lab work and a Wiki is a great way to share and seamlessly update information in groups - or just for yourself. Probably the most sophisticated Wiki software is MediaWiki, a set of PHP scripts that is under continuous development by the Wikimedia foundation; it is the same software that runs Wikipedia. This is open source, free software that is easy to install, is well documented and requires very little resources other than a machine that runs a MySQL database server and an Apache Webserver. Numerous extensions exist (and extensions are not hard to write); they enhance the already rich functionality. But let's start with small steps. By now, you should already have an account on the Student Wiki, and I have configured the Wiki so that

• only logged in users can view the pages;
• all logged in users can create and edit pages at will.

This means you could edit pages that don't "belong" to you. Respect the "House Rules" and don't edit other's things without permission, even if you can think of a particularly witty comment or hilarious prank. If you want to comment on a page: every page has an associated "Discussion" page that you can freely edit. Remember to "sign your name" to discussion entries.

Task:

• Access the Student Wiki;
• log in and navigate to your user page;
• open the "Help" link in the left-hand sidebar in a separate tab;
• follow the link to the "Editing" page on the Student Wiki;
• try and learn basic editing syntax by editing your User Page:
  • enter your name,
  • your major(s), specialist program, year of study - or your lab and thesis theme if you are a graduate student;
  • and your eMail address.
  • Add a category tag to your User page (see above) . All pages with this tag are accessible via the link in the sidebar.

Feel free to look at my User Page for code examples: clicking on the edit link will show you the source text. How do you find my User Page? Good question ...

• Create a subpage to your User Page; call it "Resources" or something similar. Note: the link MUST be in your "User space". If you don't add the prefix User:yourname/... before your page name, the new page will end up in the main "namespace". I'll then have to delete it. That's not good because you have then failed this part of the assignment. Make sure you know what you are doing, for example by looking at the code on my User Page, asking someone who knows, or asking on the mailing list.
• Put some text on your new page - perhaps a link to a Wikipedia article, or to PubMed, or to the NCBI. Make sure you understand the difference between an internal link and an external link (they have slightly different formats), and you understand the concept of namespace and categories. Also add a category link to that page.
• Play around some more. Feel free to ask how to go about achieving a particular effect that you may have seen elsewhere.

Before you are done, you should be comfortable with the following mark-up conventions and concepts:

• Login and accessing your user page;
• viewing a page's history;
• basic text formatting;
• "signing" your name;
• creating internal and external links;
• creating sections headers on a page on multiple levels;
• reverting a changed page to an earlier version;
• creating a new page (as a subpage of an existing page);
• the concept of namespaces - especially the default ("main") and User: namespace;
• the concept of categories.

I expect that there may be aspects of the Wiki you find puzzling, it is after all a complex piece of software that supports the world's largest collaborative project and one of the busiest sites on the Internet. Do ask about these things on the mailing list. My first encounter with Wikis is a while back and I can't remember everything I was initially confused about.

Pre-reading

We will discuss function annotation in our next class. The Ranganathan lab has just published a state-of-the-art pipeline for automated annotation in genome data. This is a methodological paradigm, accordingly, focus on the methods in your reading.

Islam et al. (2014) Protannotator: a semiautomated pipeline for chromosome-wise functional annotation of the "missing" human proteome. J Proteome Res 13:76-83. (pmid: 24313344)

[ PubMed ] [ DOI ] The chromosome-centric human proteome project (C-HPP) aims to define the complete set of proteins encoded in each human chromosome. The neXtProt database (September 2013) lists 20,128 proteins for the human proteome, of which 3831 human proteins (∼19%) are considered "missing" according to the standard metrics table (released September 27, 2013). In support of the C-HPP initiative, we have extended the annotation strategy developed for human chromosome 7 "missing" proteins into a semiautomated pipeline to functionally annotate the "missing" human proteome. This pipeline integrates a suite of bioinformatics analysis and annotation software tools to identify homologues and map putative functional signatures, gene ontology, and biochemical pathways. From sequential BLAST searches, we have primarily identified homologues from reviewed nonhuman mammalian proteins with protein evidence for 1271 (33.2%) "missing" proteins, followed by 703 (18.4%) homologues from reviewed nonhuman mammalian proteins and subsequently 564 (14.7%) homologues from reviewed human proteins. Functional annotations for 1945 (50.8%) "missing" proteins were also determined. To accelerate the identification of "missing" proteins from proteomics studies, we generated proteotypic peptides in silico. Matching these proteotypic peptides to ENCODE proteogenomic data resulted in proteomic evidence for 107 (2.8%) of the 3831 "missing proteins, while evidence from a recent membrane proteomic study supported the existence for another 15 "missing" proteins. The chromosome-wise functional annotation of all "missing" proteins is freely available to the scientific community through our web server (http://biolinfo.org/protannotator).

Gene ontology

An Introduction to the Gene Ontology