Fuzzy Fonts Gone

Posted on May 19, 2012 by hsauro
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Embarcardero has had some difficulties in releasing issue free versions of their new cross-platform development tool XE2. One of the most visible was the inability to display clear fonts in controls.

Most noticeable was the TMemo control which can be used to display large chunks of text. The image below shows how fuzzy the fonts were which essentially made the new cross-platform XE2 unusable.

Finally Embarcardero released a hot fix to update 4 this week which appears to fix the problem. If you have an application and you wish to avoid fuzzy fonts, add the following two lines to the start of your application:

GlobalUseGDIPlusClearType := True;
GlobalUseDirect2D := False;

And with that a screenshot of the previous application becomes:

which is a little bit better than the previous version. The fonts render better still if you choose the non-cross-platform controls base on the VCL framework, see image below:

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Announcing the iPancreas

Posted on May 1, 2012 by hsauro
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A friend of mine (Martyn Green) decided he could help out with the marketing of the Microryza project. One of the possible applications of this project is to replace biological control systems in the human body, for example replacing glucose detection and insulin secretion with a computer. The image below shows one possible application where the pancreas has been replaced by a Sinclair ZX81. Introducing the iPancreas:

Battery life might be a problem but the daily replacement of the 9v DC battery required to power the ZX81 could be easily rendered with a Kangaroo like pouch inserted into the torso area enabling easy access. The software would be written in ZX81 Sinclair Basic allowing not only reliable control of glucose levels in the patient but also optional game playing, such as 3D Monster Maze or Frogger, via an external monitor connector.

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Teaching Teachers about Synthetic Biology

Posted on April 24, 2012 by hsauro
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Natalie Kuldell is an accomplished instructor at MIT where she teaches biological engineering, including synthetic biology and design. She has also recently set up the BioBuilder web site which is geared towards providing educational and other resources for the synthetic biology community. In addition to her many other activities she has also started introducing high school teachers to synthetic biology during a week long workshop. You can find a recent interview with Natalie Kuldell at Nature EdCast where he talks more about here work.

The image below shows one experiment the high school teachers carried out. Some of you may recognize the TinkerCell logo in the petri dish formed out of bacteria that have a gene turned on in the presence of light.

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The myth of the long lasting CFL light bulb

Posted on April 14, 2012 by hsauro
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In my basement I have about 8 ceiling lights that use low energy GE CFL 23 watts bulbs. Over the last 2 years, at least 18 of them have failed. GE claims that each one should last about 8 years before failure.

Here’s a selection of the burned out ones I kept:

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Crowd Funding: Microryza

Posted on April 11, 2012 by hsauro
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There is a new crowd funding site has just started that specializes in funding research. Called Microryza, the organization aims to focus on funding risky research projects or educational outreach efforts. Yours truly submitted one of the first projects (no affiliation to the company) to build an interactive and modular electronic system to explore gene regulatory networks. Check it out and if you’re interested you can contribute as little as $1.

The picture below shows a hybrid analog/digital computer constructed by Darren Roblyer in my lab that we built a few years ago. It simulates the action of the MAPK cascade with feedback.The components circled in red are the relays that can be used to switch on and off the negative feedback and the analog circuit to implement feedback is just to the right of the relays. The components in yellow are digitally controlled resistors that can be used to control some of the binding constants in the signaling pathway (particularly the feedback strength). The board in green is one of four boards, where each board represents a Michaelis-Menten enzyme modeled as an analog system, two kinases and two phosphatases. Finally the blue box with the pink outline is the analog/digital interface to a desktop computer.

Now we want to build analog gene circuits but this time we want to use a modular design where each module represents a single gene. We will provide external connectors that will allow modules to be hooked up in different ways and thus allow someone to build a entire network of genes. Each module will have a bar graph output to indicate the level of protein the gene is making together with control knobs to change the binding constant of the controlling transcription factor and the degradation rate of the protein. Once finished we will provide professionally made circuit boards plus a component list so that anyone can build one themselves.

Posted in Electronics, Enzyme Kinetics, General Interest, General Science Interest, Modeling, Synthetic Biology, Systems Theory | Leave a comment

Nature Precedings Closes

Posted on March 30, 2012 by hsauro
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I just received an email this morning telling me that Nature Precedings (Nature’s preprint service) is closing down at the beginning of April, 2012. Shame on you Nature. No reason was given. This is what happens I supose when we rely on for-profit organsizations to support academic publishing. Obviously it’s in their right as an independent company to do as they wish and I guess it’s the risk we take if we use their services. But still, it leaves one wondering how much trust we should place in for-profit publishing companies (see also http://thecostofknowledge.com/).

The good news is that there are still at least two other organizations that support a preprint service, namely the venerable arXiv located out of Cornell University and now also figshare what is supported by Digital Science. Figshare is a “a community- based, open science project that will retain its autonomy whilst receiving support from the division.”, hopefully as a result it won’t go the way of Nature Proceedings.

Long live open publishing.

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Jim Burns’ Ph.D Thesis

Posted on March 27, 2012 by hsauro
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Why on earth should anyone would want to download a Ph.D thesis that is now almost 40 years old and presumably way out of date and completely irrelevant in today’s terabyte data world? Well for one, Jim’s thesis is an important historical document relating to the origin of Metabolic Control Theory (MCT). For those who don’t know, MCT (or BST as developed by M. Savageau) is the first, clear, practical and theoretically useful treatment of complex cellular enzyme networks. In a sense it continues where enzyme kinetics becomes unmanageable though it uses a completely different approach. One of the nice aspects of MCT is that it is actually quite simple and is amenable to anyone with a basic understanding of differential calculus. Anyone who calls themselves a scientist with have this knowledge, those who don’t can’t. Those who dismiss MCT or pass over it without much thought have pretty much missed the point. What is the point? Well…..

  • It’s a formal language to describe complex cellular networks.
  • To those who are willing to spend time studying MCT, it forces clarity of thought.
  • It connects genome and environment with phenotype.
  • It helps to uncover the cause and effects in a complex system; who does what, how and why.
  • It helps to give direction in the search for novel drug targets and the rational manipulation of metabolism.

What I find most remarkable about Jim’s text is it’s modern feel which suggests that the content was decades ahead of his time. One finds in the thesis work that was anticipated by later workers, even results which were later presented, unknowingly of course, as novel by subsequent researchers. So I hope the thesis will be of interest, not only for historical reason but also as a source of inspiration for future work.

Here is the thesis

I am grateful to Jim Burns for allowing me to upload the text of his thesis. Also thanks to Jannie Hofmeyr who assisted in the conversion process.

Posted in Enzyme Kinetics, General Science Interest, Metabolic Control Analysis, Modeling, Pathways, Systems Theory | Leave a comment

Never say never….

Posted on March 21, 2012 by hsauro
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Someone posted these quotes in response to a skeptic’s comment that solar, wind and other renewable energy sources will never economically match petroleum, coal or nuclear:

“Man will never reach the moon regardless of all future scientific advances. –Dr. Lee DeForest, “Father of Radio & Grandfather of Television.”

“The bomb will never go off. I speak as an expert in explosives.” –Admiral William Leahy, US Atomic Bomb Project

“There is no likelihood man can ever tap the power of the atom.” –Robert Millikan, Nobel Prize in Physics, 1923

“I think there is a world market for maybe five computers.” –Thomas Watson, chairman of IBM, 1943

Meanwhile:

Startup Aims to Cut the Cost of Solar Cells in Half

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Analog Computers

Posted on March 15, 2012 by hsauro
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Although I was brought up on digital computers I have quite a soft spot for analog computers. I used to have an old web page that had some notes and pictures plus some rare analog construction notes that I copied from a 1978 article I had. I thought I’d rejuvenate the page and notes here.

The digital computer is a sequential device, in general, operating on data one step at a time, in addition the digital computer represents data internally using a verbose but very robust form of representation called binary. Thus a single transistor in a digital computer can only store two states, on and off. Obviously to store a number to any sensible degree of precision, many transistors are required.

An analog computer operates in a quite different way. For a start, all operations in an analog computer are performed in parallel. Secondly, data are represented in an analog computer as voltages, a very compact but not necessarily robust form of storage (prone to noise corruption). A single capacitor (equivalent to the digital’s computer use of a transistor) in an analog computer can represent one entire continuous variable.

EC-1 Educational Analog Computer, introduced in 1960 by Heathkit.

The Heathkit Educational Analog Computer is completely self-contained and contains nine DC operational amplifiers with provision for balancing without removing problem setup. It also features three initial condition power supplies, five coefficient potentiometers, four sets of relay contacts, an electronically regulated power supply and a built-in repetitive oscillator for automatic operation. The complete EC-1 kit also contains an assortment of precision resistors, capacitors, special silicon diodes and patch cords for setting up scores of complex computer problems easily and accurately.

Vannevar Bush’s differential analyzer

(Image from http://archive.computerhistory.org/)

The first mechanical/electrical analog computers were developed in the early part of the 20th century. One of the most well known of these was the Vannevar Bush’s differential analyzer that filled a room at the Massachusetts Institute of Technology. Vannevar Bush’s differential analyzer crunched through calculus in seconds, although technicians often spent hours setting it up to solve an equation. A multitude of wheels, discs, shafts and gears handled the computations with precision unmatched by any contemporaneous machine. With the advent of the digital computer after World War II, the development of the analog computer slowed and by the early 1970s it was being rapidly supplanted by digital machines. One wonders whether with today’s electronic technology the analog computer might reemerge as a general purpose computer.

Designs for Analog Computers

Practical Electronics (UK), 1978
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Favorite Quotes

Posted on March 11, 2012 by hsauro
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I was reminded again the other day of one of my favorite quotes which relates directly to one of the potential pitfalls of mathematical modeling. I thought I would repeat the quote here but also give another quote that rings true for today’s metabolic engineers from Monod, 1949.

Suárez Miranda, Viajes de varones prudentes, Libro IV, Cap. XLV, Lérida, 1658

Borges, J. L. 1998. On exactitude in science. P. 325, In, Jorge Luis Borges, Collected Fictions (Trans. Hurley, H.) Penguin Books.

“On Exactitude in Science….

… In that Empire, the Art of Cartography attained such Perfection that the map of a single Province occupied the entirety of a City, and the map of the Empire, the entirety of a Province. In time, those Unconscionable Maps no longer satisfied, and the Cartographers Guilds struck a Map of the Empire whose size was that of the Empire, and which coincided point for point with it. The following Generations, who were not so fond of the Study of Cartography as their Forebears had been, saw that that vast Map was Useless, and not without some Pitilessness was it, that they delivered it up to the Inclemencies of Sun and Winters. In the Deserts of the West, still today, there are Tattered Ruins of that Map, inhabited by Animals and Beggars; in all the Land there is no other Relic of the Disciplines of Geography.”

From THE GROWTH OF BACTERIAL CULTURES BY JACQUES MONOD Annu. Rev. Microbiol. 1949.3:371-394.

“It has often been assumed that the over-all rate of a system of linked reactions may be governed by the slowest, or master, reaction. That this conception should be used, if at all, with extreme caution, has also been emphasized (17, 18). On theoretical grounds, it can be shown that the over-all rate of a system of several consecutive reversible enzymatic reactions depends on the rate and equilibrium constant of each. The reasons for this are obvious, and we need not go into the mathematics of the problem. A master reaction could take control only if its rate were very much slower than that of all the other reactions. Where hundreds, perhaps thousands, of reactions linked in a network rather than as a chain are concerned, as in the growth of bacterial cells, such a situation is very improbable and, in general, the maximum growth rate should be expected to be controlled by a large number of different rate-determining steps.”

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