SOFTWARE CARPENTRY WORKSHOP @ EMBL

What: A course for life scientists who do data analysis
Where: EMBL (Heidelberg, Germany)
When: 12-14 November 2014
Apply by: 26 September 2014

This course is open to researchers in the life sciences who are using computers for their analyses, even if not full time. The target student will know a little bit of data analysis, but not consider himself an expert. For example, the student might have already written a for loop in some language before or plotted their data, but will not know what git is (or at least not be very comfortable with advanced git usage).

TOPICS

  • Introduction to Python scripting
  • Introduction to the Unix shell and usage of cluster resources
  • Version control with git and github
  • Unit testing

More information:
http://www.embl.de/training/events/2014/SWC14-01/
http://software-carpentry.org/

Tuesday Links

Posting today from the lovely KU Leuven campus (yes, this link points to the actual building where I’m sitting in now!).

  1. From Megan McArdle on why very invasive surgery works better than less invasive surgery:

    Patients may prefer percutaneous coronary intervention — also known as angioplasty — to a coronary bypass because it doesn’t involve cracking your chest open and grafting things onto your heart. But bypass patients seem to have better long-term outcomes, even though both methods increase blood flow to the heart muscle. [...]

    A new working paper from the National Bureau of Economic Research suggests a possible answer: Bypass works better precisely because it’s more invasive. The very scale of the treatment makes people more likely to change their post-operative behavior in ways that enhance their long-term chances of survival

The original paper states that

We find that CABG patients are 12 percentage points more likely to quit smoking in the one-year period immediately surrounding their procedure than PCI patients, a result that is robust to numerous alternative specifications

  1. I have in the past criticized nutricional sciences, but this is excellent scientific behaviour

    In one of the best examples of science working, a researcher who provided key evidence of (non-celiac disease) gluten sensitivity recently published follow-up papers that show the opposite.

    [...]

    For a follow-up paper, 37 self-identified gluten-sensitive patients were tested [...]

    The subjects cycled through high-gluten, low-gluten, and no-gluten (placebo) diets, without knowing which diet plan they were on at any given time. In the end, all of the treatment diets — even the placebo diet — caused pain, bloating, nausea, and gas to a similar degree. It didn’t matter if the diet contained gluten.

One of the most insidious things about some of the health fads is that because of psychological effects, they do “work.”

3. Python San Sebastian will have a keynote talk & tutorial by your truly (it’s not up on the website yet, but it will be).

 

Auto text

This is what I got from running the text predictor on my phone (which has been, at least partially, trained on my texting/email writing):

I am having trouble getting tickets online now from our large stock inventory of the meal and a half years ago and I will be at the moment and I will be at the moment and I will be at the moment and I will be at the moment and I will be at the moment and…

Then it goes into an infinite loop.

Thursday Links

Lazy August links:

  1. Ray, the parking robot:

    [T]he system could work fine without any human oversight, but the airport is having an employee on hand in case travelers have questions about how to use the new option.

  2. OKCupid experiments on human being! But because they don’t publish in scientific journals and do it just for fun and profit, that’s totally OK (unlike the facebook study, which was unethical because they published).

Friday links

  1. A last link on the facebook saga makes the observation that if facebook just includes some randomness in all decisions of what to show on the stream (which they might do just to improve their service), then any study which leverages this is a randomized observational study. And observational studies have much reduced ethical thresholds.

  2. An excellent summary of what is known about SSRIs. I really liked both the conversion of effect size to weight loss numbers and the discussion of how, whilst people can agree on the data, it gets very hairy when you start to use words such as “moderate depression” or “severe depression” to describe different numeric results.

  3. Some people who make more money than I do, can activate your DNA. Obviously, they are skeptical of ENCODE claims. This guy’s biography is perfect:

    Toby Alexander, is a coach, speaker, seminar leader and author. He is a leading expert in a variety of fields including energy medicine, emotional mastery, peak mental strategies for optimal performance, 15th dimensional physics, futures and forex trading, SAP, remote viewing, and distant healing.

  4. Next week, I’ll be in Lisbon for LxMLS 2014. Contact me if you want to get in touch there.

New Paper: Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo

(This is a guest post by Ana Pena, who is  the first author of Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo, a paper I had a small hand in).

 

Pena_Paper_Figure3(Panels A & B from Figure 3 in the paper, showing effects of RNAi knockdown of H1)

The organization of DNA inside the eukaryotic nucleus relies on what we like to call the “beads-on-a-string” structure of chromatin, in which nucleosomes are the “beads” and DNA is the “string” around. While we already know a lot about the histones that make up the nucleosome, the functions of the “extra” histone, histone H1, only now start to be uncovered in vivo.

Histone H1 is a small protein that sits outside the nucleosome “beads” and binds to the DNA between them. In this work we explored the role of histone H1 in Trypanosoma brucei, a unicellular parasite responsible for Sleeping Sickness. Genome-wide RNA expression revealed an interesting fact in this parasite: histone H1 acts mainly as a repressor of a particular cohort of genes, which are transcribed by RNA polymerase I and are essential for its differentiation and survival inside the host. To understand if histone H1 represses transcription at these loci, we performed metabolic labeling of nascent RNAs with 4sU for the first time in this parasite, showing that histone H1 silencing effect is exerted at the transcriptional level.

Full paper citation

Pena AC, Pimentel MR, Manso H, Vaz-Drago R, Neves D, Aresta-Branco F, Ferreira FR, Guegan F, Coelho LP, Carmo-Fonseca M, Barbosa-Morais NL, Figueiredo LM. “Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo”. Mol Microbiol, 2014 Jun 19. doi: 10.1111/mmi.12677.