I believe many lab robots are scrapped purely because the control computer and the control software become obsolete. With the ability to write new software such robots can become useful again, and not only in DIY-bio settings. There is however very little documentation as far as I can see. I had opportunity to experiment for a weekend with an Ettan Spot Picker lab robot, and found that reverse engineering its communication protocol was not very hard. Unfortunately most of my documentation in text files and programs were eventually lost together with the old command computer of the robot, as I forgot to move them off. I hope what is left can be still of some help in starting, if someone is in a similar situation.

An Ettan Spot Picker (Wikimedia Commons).

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Some drawings made by a repurposed lab robot (an old Ettan Spot Picker to be disposed of), using a mechanical pencil. It became a universal robot arm (and thus an able draughtsman) after some reverse engineering of the communication protocol.

Pencil lead run out at some point . . .

Having freshly drawn XKCD comics instead of having to view them on a screen is of course luxurious. Never shall there be a shortage of mazes to fill out either. With the recursive division algorithm the robot can draw an infinite number of different mazes.

Many thanks to the Proteomics group for offering their old machine for some experimenting.

The Royal Society celebrated its 350th anniversary last year. Trailblazing is a collection of historic papers, which the society published in her Philosophical Transactions. Here some favourites. Each is a very early paper of its field, so everything has to be explored, new things need to be named, nobody knows which are the relevant parameters.

• … New Theory about Light and Colours… (1672) Isaac Newton at his best: buys a prism, uses the sun, his window curtains and a ruler to deduce the corpuscle theory of light, a theory of the nature of colours, of mixture of colours, of white light, the mechanism of colour vision, the inner workings of rainbows, and the limitation of refractive telescopes due to colour dispersion. He also invents the reflective telescope to overcome the problem. He does not waste time with a splendid introduction: To perform my late promise to you, I shall without further ceremony acquaint you, that in the beginning of the year 1666 I procured me a Triangular glass-Prisme to try herewith the celebrated phenomena of colours. and comes to his experiments right away. A very enjoyable reading. Continue reading →

Finite state machines for fun & profit. A python snippet which extracts titles and sequences from FASTQ files and discards the rest.

reader = open("humanrna.fastq", "rb")
title=""
buffer=""

while 1:
    line = reader.readline()
    if not line:
        break
    line = line.strip()

    if line == "":
        continue

    if line.startswith("@"):
        #this is a title -- starts a new fastq block
        title=line[1:]
        #read seq
        buffer = reader.readline().strip()
        #dump quality control
        dummy = reader.readline()
        dummy = reader.readline()

       #some use of title and buffer...
       # ...

A snippet for reading FASTA files.

reader = open("humanrna.fasta", "rb")
title=""
buffer=""

def useBuffer(title, buffer):
    #use the buffer somehow...
    #...
    pass

while 1:
    line = reader.readline()
    if not line:
        #This is the end
        if title:
            #use the last title and buffer...
            useBuffer(title, buffer)
        break
    
    line = line.strip()

    if line == "":
        continue

    if line.startswith(">"):
        #this is a title -- starts a new fasta block         
        if buffer:
            #use the last title and buffer somehow...
            useBuffer(title, buffer)

        buffer=""
        title=line[1:]
        continue                    

    if title:
        buffer += line

A little toy tool that shows which logic functions are compatible with the observed behaviour of a logic gate, e.g. when making a boolean model of an enhancer out of loss-of-function data. Created for fun during a summer school on genetic networks in Woods Hole.

• for 2 input variables
• for 3 input variables

In each row:

• input field: response of gate (1/0)
• grey coloumns: state of input variables
• remaining orange coloumns: compatible logic functions.

If you are looking for last year’s CUCC (Cambridge University Caving Club) accounts, they are now here.

Experiments to Determine the Density of the Earth (1798): Henry Cavendish’s heroic struggle for precision as he improves John Michell’s apparatus such that for the first time he is able to measure the gravitational constant exactly. For that he measures the minuscule attraction of two weights. From this he calculates the gravitational force per mass and such is able to calculate (“weigh”) the earth’s mass and incidentally of all parts of the solar system. 

The Royal Society is celebrating its 350th anniversary. Trailblazing is a collection of historic papers published in the Philosophical Transactions by the Society. Here my first favourites, all of them trying to find relevant parameters for the description of new phenomena:

• … New Theory about Light and Colours… (1672) Isaac Newton at his best: buys a prism, uses the sun, his window curtains and a ruler to deduce the corpuscle theory of light, a theory of the nature of colours, of mixture of colours, of white light, the mechanism of colour vision, the inner workings of rainbows, and the limitation of refractive telescopes by colour dispersion. He also invents the reflective telescope to overcome the problem. He does not waste time with splendid introductions: To perform my late promise to you, I shall without further ceremony acquaint you, that in the beginning of the year 1666 I procured me a Triangular glass-Prisme to try herewith the celebrated phenomena of colours. and comes to his experiments right away. A very enjoyable reading.
• …Little Animals by Him Observed in Rain-Well-Sea and Snow Water… (1677) Antoni van Leeuwenhoek uses his newly constructed microscope on water from different sources and ubiquitously finds a universe of little beings. He doesn’t quite understand yet where all he sees is coming from. Still he describes very vividly the struggle and happiness of swarming and multiplying “animaculi”.
• An Electrical Kite (1752) Benjamin Franklin flies in a bold experiment a kite before a thunderstorm and discovers a charge difference between ground and sky. He deduces that lightnings are but large sparks and that lightning conductors might be a good way to tame them.
• Observations on Different Kinds of Air (1772) Joseph Priestley kills rodents, birds and plants in gasses of colourful origin and eventually his reader’s attention with endless descriptions. This to work out, what gasses might be at all, how they connect beer, fire, breathing and green plants, and how to purify some of them. Unfortunately he has limited success with the latter aim and works usually with quite crude mixtures.

If you are a member of Ludwig-Maximilians-Universität or Technische Universität in Munich and retrieve lots of journal papers behind paywalls this bookmarklet might make your life easier: 

ToDocWeb

Drag the link into your bookmarks toolbar and click on it every time you encounter the paywall of a university-subscribed journal. On click the bookmarklet transcribes the URI and reloads the page via the LRZ DocWeb webproxy which gives you access to most journals (you will need to log in). This without a VPN connection or traversing Elektronische Zeitschriftenbibliothek first when you start DocWeb from the LRZ homepage.