My new go-to for cheap PCBs: Seeed studio

Full disclosure: Seeed studio emailed me and said I'd get a $30 coupon if I wrote a review of my experience ordering PCBs from them. Edit: May 3, 2017 - they have since delivered on this promise, so I've got $30 to spend on new boards! Sweet. Definitely my new source for pcb manufacturing.

First off, I usually order 2-layer boards, and I'm not pushing the fab limits at all (usually my minimum clearance and trace widths are both >12 mil). My bottom line is price, since I pay for the stuff myself, and I'm a postdoc (hence I'm not rich).

In the past, I've ordered PCBs from Sunstone and Advanced Circuits (4PCB). Mostly, I care about price. At advanced circuits, for $33 I can get a seemingly arbitrarily large 2-layer board (only available to students, otherwise the minimum order quantity is 4), but if I tile a small PCB so that I can get 10 small PCBs for the price of one, then they slap on a $50 array fee. And then there's shipping (which for some reason is always really expensive, like >$20) so the minimum cost is about $50 for a single PCB. Sunstone used to be significantly more expensive, but I recently ordered some boards there for around $50 each.  So, similarly priced.

Recently, a friend of mine told me about Seeed studio. They are fantastically priced - I bought ten 2.2-square-inch boards (2-layer) for $15 there (plus an $18 shipping fee).

I received the board 9 days after ordering - comparable to sunstone and advanced circuits. Quality-wise they're clearly a little bit below sunstone and advanced circuits, as there are minor misalignments in the silkscreen and the soldermask. But so far as I can tell with my first batch, totally functional. Definitely will order again (and update this post if I find any further issues!)

 

New goal

For every dollar I spend on alcohol, I'm going to donate that same amount to a charity.

Are bacterial mutation rates higher in space?

Apparently Nanobiosym, a biotech company in the area, has decided to send MRSA up to the ISS on a spacex rocket. This is headline-grabbing stuff. From the NASA page:

Proof-of-Concept for Gene-RADAR® Predictive Pathogen Mutation Study (Nanobiosym Genes) evaluates the feasibility of one day using this device from Nanobiosym® to identify bacterial mutations in space. The X Prize-winning device can accurately detect any disease that has a genetic fingerprint, in real time and at the point-of-care. Microgravity may accelerate the rate of bacterial mutations and this pilot investigation analyzes this process in two strains aboard the International Space Station, which may provide insight into how deadly bacteria become drug-resistant.

(Source: https://www.nasa.gov/mission_pages/station/research/experiments/2420.html)

Seriously, what????? $20 to anyone who can provide a reasonable and nontrivial explanation (e.g. not like, the cultures were less aerated in space because they weren't on a shaker) for why microgravity would accelerate the rate of bacterial mutations.

From a Salon.com article, Anita Goel (founder of Nanobiosym) is quoted as saying “[Low Earth Orbit] acts as an incubator to accelerate the mutations that happen with some  bacteria and viruses”.

That makes no sense at all to me. Can anyone explain?

Correlations in time series are sensitive to timescale

... and it's something that perhaps we don't look at quite often enough!

What am I talking about? Well, let's imagine that we're interested in the relationship between two signals, , and . One of the most basic analyses we might do is ask "are they correlated?" But perhaps the correlation depends on the timescale that we focus on. Could a signal be positively correlated at once timescale and negatively correlated at another scale?

Since I've shown you an example, hopefully you believe that a signal could be positively correlated at one timescale and negatively correlated at another! Here, and are positively correlated on a long timescale but negatively correlated on a short timescale.

Can we characterize this sort of relationship? Yes, and I'll outline one way of characterizing this sort of time-scale dependent correlation below.

Continue reading "Correlations in time series are sensitive to timescale"

Paper #20 - Specific roles for DEG/ENaC and TRP channels in touch and thermosensation in C. elegans nociceptors

Title: Specific roles for DEG/ENaC and TRP channels in touch and thermosensation in C. elegans nociceptors

Year: 2010

Summary:

Here they were interested in discovering which proteins mediate nociception - the sensation of pain. Neurons that detect pain are referred to as nociceptors, and are thought to be multimodal - that is, they respond to many kinds of sensory inputs that generate pain, like heat, cold, harsh touch, extreme pH, or noxious chemicals. This paper seeks to answer the question of how nociceptors obtain their multimodality. Do they have single receptors that respond to all these inputs? Or do they have many receptors? At which point do these sensory inputs converge onto the same signal transduction path?

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My top 54 functions to know when using R

I was trying to figure out what I'd want to know if I were just learning R, and I think these might be my favorites. The list is not complete, and I welcome suggestions! I will also try to add some documentation to this so that it could be printed out and used for reference.

  1. ls
  2. rm
  3. library
  4. install.packages
  5. list.files
  6. getwd, setwd
  7.  apply
    • mapply
    • sapply
    • lapply
  8. str
  9. dim
  10. colnames
  11. rownames
  12. names
  13. summary
  14. %in%
  15. which
  16. c
  17.  plot
    • points
    • lines
  18. image
  19. matplot
  20. hist
  21. heatmap
  22. density
  23. par
  24. layout
  25. legend
  26. text (mtext?)
  27. t
  28. na.omit
  29. read.table
  30. write.table
  31. as. (as.character, as.numeric, as.matrix...)
  32. data.frame
  33. aggregate
  34. merge
  35. reshape
  36. order
  37. sort
  38. cbind/rbind
  39. lm
  40. nls
  41. optim
  42. unique
  43. sum
  44. cumsum
  45. diff
  46. setdiff
  47. intersect
  48. rnorm
  49. sample

Paper #19 - Natural light-gated anion channels: a family of microbial rhodopsins for advanced optogenetics

TitleNatural light-gated anion channels: a family of microbial rhodopsins for advanced optogenetics

Year: 2015

SummaryIn this paper, they're interested in finding new optical actuators for controlling the membrane polarization of the cell (and particularly neurons). they begin by investigated a class of class of rhodopsins from cryptophytes, as opposed to previous channelrhodopsins which have been obtained for chlorophytes (green algae). Cryptophytes are also algae, but in a different kingdom (chromalveolata) than green algae (archaeplastida), thus they're probably quite significantly diverged.

They focus very quickly and with little justification (probably not their fault, Science doesn't provide much space) on  Guillardia theta, a cryptophyte alga with a fully-sequenced genome. In this genome, there are 53 proteins sharing similiarity to microbial rhodopsins.

Continue reading "Paper #19 - Natural light-gated anion channels: a family of microbial rhodopsins for advanced optogenetics"