One of the first things we looked at was the trending terms on twitter; Specifically, for every day over the last 6 months. I made some fun aggregate visualizations of this with whiskerplots using topfunky’s sparklines gem in ruby: here’s the top 100 trends, and here’s the top 2000. (here’s the code.)

8 twitter trends from 1-jan-2009 to 5-jun-2009

That was all weeks ago, though. Today is a happy day for the WEP because today, we published our first report: Iranian Election and Twitter: The First Eighteen Days. I only contributed a little bit to some of the early twitter stats (I’ll write more about them later) – David Fisher and others were the real hard workers.

From June 7 – 26, we recorded 2,024,166 tweets about the election in Iran, and we found out some pretty interesting things. Guess how many of those 2 million tweets were retweets! Go check out the report to find out (pdf).

Iranian Election and Twitter: The First Eighteen Days

Unfortunately, I dislike reading PDFs on my computer screen – I would like to access the library on a smaller, more portable, preferably e-ink device. I have a kindle 1 and an OLPC, both of which have the smaller form factor and tablet mode that I like. Unfortunately, the kindle 1 does not support PDF and my attempts at converting journal articles and textbooks have been unsatisfactory and unreliable at best.

OLPC vs. Kindle 1

I would love to use the kindle, since it can provide ~8000 pages on a single 3-hour battery, is very light, and has a great screen, but I would be limited to whatever I could fit on an SD card (SDHC is unreliable but may work), and if I had converted the PDFs into images, I would lose the ability to search the content.

The OLPC seems more promising. It’s not light enough to comfortably hold for long periods of time, but I usually can find a way to prop it up on a knee or table. The battery only lasts 4 hours or so on a full charge, but it can natively display PDFs in tablet mode and has a remarkable screen that approaches e-ink in clarity (although not viewing angle). It can run debian & gnome, and I feel like there has got to be a good application out there for that environment built for managing large document collections and searching across them. It has like 2GB of built-in flash memory for the OS and an SDHC slot.

I’ve taken some photos comparing the screens of the OLPC natively showing a PDF and of the Kindle 1 showing a .prc file of the same PDF converted with PDFRead.

Basically, I want iTunes for PDFs on Linux. With fast full-text search.

Oh, I have my eye on the Kindle DX and the FoxIt eSlick e-ink readers. Both can display PDFs natively.

Here’s a short screencast I made demonstrating how I like interact with my pdf library.

(Download the source of this video from vimeo for more detail – it’s only 60 megs and is 1280×720)

Part 1: Spatiotemporal Transcriptional Logic

Consider the marvelous spatiotemporal program an organism’s genome must encode to organize embryogenesis and development.  Cells divide and specialize, divide and specialize, recursively executing the developmental program stored in the genome according variables mediated by time and space.

This process is reliable and repeatable: for instance, (under normal growth conditions), wild-type C. elegens develops into precisely 959 somatic cells, for each of which the lineage and developmental fate is known.   The implications continue to amaze me – is development really so deterministic?!

Davidson College’s Genomics class introduced the notion of spatiotemporal logic with an in-depth analysis of the genetic control regions of a Sea Urchin gene called Endo16.  Eric Davidson’s lab essentially spent years reverse engineering the genetic logic controlling Endo16′s expression in developing Sea Urchin embryos.  They elucidated the identity of modular patterns of regulatory DNA upstream of Endo16.  These regulatory modules act as inputs for a variety of transcription factors.  To understand the transcriptional logic encoded by the pattern of regulatory modules, the Davidson team quantitatively measured the effect different transcription factor combinations had on the output of the regulatory region i.e. expression of Endo16.   The logic they deduced was so coherent they were able to write it in pseudocode.

Here is a diagram from one of their papers describing the transcriptional logic:

Let me quote from the introduction of their paper:

Each gene, in each cell of a developing animal, must read and respond to the presence or absence of multiple inputs. In effect, these inputs provide the gene with the regulatory information it requires to determine its own activity: this includes signaling inputs from adjacent cells and inputs that indicate what other relevant genes have been functioning in the cell in which the gene resides. These inputs are presented to the gene in terms of concentrations and activities of nuclear transcription factors. The heritable structural basis for cis-regulatory information processing functions consists of the target site sequences at which transcription factors bind to the DNA. The identity and disposition of these sites specify the regulatory activities that can be executed by the cis-regulatory system, depending on circumstances. This genetic hardwiring causally determines to which inputs each gene regulatory system will (Davidson, 1990; Davidson, 1999; Davidson, 2001).

So essentially, the spatial and temporal variation in transcription factors are the inputs for logic gates controlling gene expression.  Sound interesting?  The next step is to check out The regulatory genome and the computer, a review the Davidson team wrote in 2007 that is in ways the genomics version of Von Neumann’s The Computer and the Brain.  I’ll leave you with the abstract:

The definitive feature of the many thousand cis-regulatory control modules in an animal genome is their information processing capability. These modules are “wired” together in large networks that control major processes such as development; they constitute “genomic computers.” Each control module receives multiple inputs in the form of the incident transcription factors which bind to them. The functions they execute upon these inputs can be reduced to basic AND, OR and NOT logic functions, which are also the unit logic functions of electronic computers. Here we consider the operating principles of the genomic computer, the product of evolution, in comparison to those of electronic computers. For example, in the genomic computer intra-machine communication occurs by means of diffusion (of transcription factors), while in electronic computers it occurs by electron transit along pre-organized wires. There follow fundamental differences in design principle in respect to the meaning of time, speed, multiplicity of processors, memory, robustness of computation and hardware and software. The genomic computer controls spatial gene expression in the development of the body plan, and its appearance in remote evolutionary time must be considered to have been a founding requirement for animal grade life.