Monday, September 06, 2010
   
Text Size
Latest:

dipchip.gifScientific computing and instrumentation

Latest news in scientific computing and development of low-cost hardware for laboratory instrumentation. The pages in this section contain links to web sites with DIY instructions for building hardware and open-source or low-cost software.


 

Arduino Mega

From: http://arduino.cc/en/Main/ArduinoBoardMega

 

Overview

The Arduino Mega is a microcontroller board based on the ATmega1280 (datasheet). It has 54 digital input/output pins (of which 14 can be used as PWM outputs), 16 analog inputs, 4 UARTs (hardware serial ports), a 16 MHz crystal oscillator, a USB connection, a power jack, an ICSP header, and a reset button. It contains everything needed to support the microcontroller; simply connect it to a computer with a USB cable or power it with a AC-to-DC adapter or battery to get started. The Mega is compatible with most shields designed for the Arduino Duemilanove or Diecimila.

   

Open source hardware 2008

The MAKE: guide to open source hardware projects in 2008 from: http://blog.makezine.com/archive/2008/11/_draft_open_source_hardwa.html

Mksp4-2What is open source hardware? Briefly, these are projects that creators have decided to completely publish all the source, schematics, firmware, software, bill of materials, parts list, drawings and "board" files to recreate the hardware - they also allow any use, including commercial. Similar to open source hardware like Linux, but hardware centric.

This is one of the new and emerging trends we've seen really take off over the last few years. Each year we do a guide to all open source hardware and this year there are over 60 projects/kits - it's incredible! Many are familiar with Arduino (now shipping over 60,000 units) but there are many other projects just as exciting and filled with amazing communities - we think we've captured nearly all of them in this list. Some of these projects and kits are available from MAKE others from the makers themselves or other hardware manufacturers - but since it's open source hardware you can make any of these yourself, everything is available.

   

High Speed Photography using the Arduino

thumb_red-green-splashthumb_high-speed-splash1Using a laser and sensor to create an electronic trip wire, this high tech photographer used the Arduino programmer to capture high speed pictures of liquid droplets, creating this outstanding collection of photographs.  His photos can be seen below, and you can learn how to make your own with the full tutorial and project code.  Some low priced lasers and other project supplies are required.

   

tikitag: RFID for your applications

tikitag

From Crave: we're huge fans of radio frequency identification (RFID) technology. Oyster cards have made our commutes less painful, RFID passports are promising to cut queues at airports, and the data logged by our office keys give us alibis when we're accused of crimes we didn't commit -- true story.

So it's no wonder we got excited when Firebox handed us the tikitag personal RFID system. This consists of a small USB scanner, rather like the Oyster readers at London train stations, and a bag of tikitags -- small stickers, which when scanned can trigger pre-programmed, PC-related tasks.

The actions of each tikitag can be changed by downloading and editing 'applications' from the tikitag Web site. At present, the majority of tikitag apps are pretty basic, but there are glimmers of promise. One application -- the Social Business Card -- lets you launch a page linking to all your social media pages. The idea is that you program multiple tikitags with this functionality, stick them on the back of your business cards, hand them out to other owners of tikitag readers, and they'll get quick online access to all your data.

But therein lies the problem -- almost nobody has a reader, and until the tikitag development community starts coming up with applications that do something a little more useful than 'scan this tag to turn your speaker volume up a bit', or 'open this Web site', not many more people will buy one.

We suggest tikitag give the £35 readers away to companies for free in order to raise awareness, and cut the price of replacement tags -- £20 for 25 is too much to ask. Perhaps doing so would raise awareness of the product, increase the size of the development community, and increase the proliferation of this potentially brilliant piece of kit.

Starter packs will be available from Firebox later this week. (from Crave UK)

   

Computer models of plant tissue growth and morphogenesis

thumb_cellmodeller2a

Cells within a plant meristem form a complex system, and clearly possess self-organising properties. However, there are few methods available for modelling the physical relationships and information exchange between these cells in a biologically relevant way. We have developed new software tools for dynamically modelling cellular morphogenesis in plants. The physical properties of cells have been modelled in 2D, using double springs to describe wall properties. This physical model provides an engine for the production of cells through enlargement and division. The CellModeller program provides an environment for combining physical and genetic descriptions of multicellular growth. Fields of proliferating cells can be programmed via a genetic script to produce and respond to different morphogens. (Haseloff Lab)

   

SciComp@Cam: Scientific Computing in Cambridge

scicomp

Computers form an important part of modern scientific research and there is high flux of new technologies and approaches that continually fuel new developments in this field. There is a large, motivated community of workers in Cambridge who are doing exciting work with advanced computer hardware and software. However the work is organised in different fields and institutions, and interdisciplinary exchange is usually difficult. 

SciComp@Cam has been set up to provide an informal forum for exchange of practical techniques and information between students, faculty and interested professionals and companies outside the University. The aim of the group is to bring together people with an interest in the interdisciplinary development and application of computers in science, and to provide a venue for sharing hands-on approaches to use of computers and application of hardware and software tools in science. Regular meetings are held at the Centre for Mathematical Sciences, and you can find linked web resources, including details of people in Cambridge, forums for exchange of news and information, special interest groups, and details of monthly meetings held by the group. Register at http://scicomp.collectivex.com for free access to an interactive forum.

Steven Eglen, DAMTP/CCBI, University of Cambridge
Alex Griekspoor, European Bioinformatics Institute,Hinxton
Jim Haseloff, Plant Sciences, University of Cambridge
Julian Huppert, Physics, University of Cambridge
Alex Kabla, Engineering, University of Cambridge
Gos Micklem, Genetics/CCBI, University of Cambridge
Chris Swain, Cambridge MedChem Consulting, MacResearch

   

The cheaposcope

thumb_ledlit

Development of a low cost fluorescence microscope for teaching. Over the last decade, biofluorescent proteins have revolutionised the study of biological processes. The ease of use of these fluorescent markers makes them especially suitable for use in teaching. However, instruments for fluorescence imaging are generally expensive.
I've experimented with recent developments in LED technology, optical filters and cameras in an attempt to construct cheaper instruments for fluorescence microscopy and detection. The following pages describe our ongoing attempts - and hope that some may find the details useful. (Jim Haseloff, University of Cambridge).

   

An automated home-built low-cost fermenter for Escherichia coli.

We have developed an automated fermentation system for cost-efficient upscaling of protein expression in bacteria. The system, built for use by nonbiotechnologists, can be assembled mostly from standard laboratory equipment and allows a largely unattended growth of bacteria to OD 25 (at 600 nm) in a 12 L vessel. The typical yield of 250-350 g of wet weight cell pellet per run, which is equivalent to the biomass obtained from 250 shake flask cultures containing 400 mL Luria-Broth medium each, facilitates the production of large amounts of purified recombinant protein without the laborious need for optimization of expression and purification conditions.

Publication Date: 2008 Aug PMID: 18687068
Authors: Riek, U. - Tuerk, R. - Wallimann, T. - Schlattner, U. - Neumann, D.
Journal: Biotechniques

   

Page 1 of 2

SciComp news

  • Compressed sensing   Fill in the Blanks: Using Math to Turn Lo-Res Datasets Into Hi-Res Samples By Jordan Ellenberg  February 22, 2010  |   12:00 pm  |   Wired March 2010 Using a mathematical...
  • Sony PS3s for supercomputer   Sony still subsidizing US military supercomputer efforts The PlayStation 3's price drop was a boon for more than just consumers. The US military is now snapping up a few thousand more of the consoles to add to its (Sony-subsidized) supercomputer....
  • 100 core processor   New Processor Will Feature 100 Cores Forget dual-core and quad-core processors: A semiconductor company promises to pack 100 cores into a processor that can be used in applications that require hefty computing punch, like video conferencing,...
  • 48-core Intel processor   Intel Shows 48-Core Processor for Research Intel’s six- and eight-core processors are the fastest chips that consumers can get their hands on. But if you are among the research elite, the company has a new experimental chip that can...
  • 1
  • 2
  • 3
  • 4
  • 5

Instrumentation news

  • DIY Photography: Laser-Triggered Camera     From: Hack A Mod (http://hacknmod.com/hack/diy-photography-incredible-laser-triggered-camera-rig/) Learn how to build an incredibly photography rig to take detailed macro photos of insects, water drops, or anything else you desire. ...
  • High speed microfluidics Microfluidics that is a Million Times Faster will enable Synthetic Biology and DNA Nanotechnology Scaling Breakthroughs   From: http://nextbigfuture.com/2010/03/microfluidics-that-is-million-times.html Caption: The microfluidic sorting...
  • DIY Macro Photography Kit on the Cheap DIY Macro Photography Kit on the Cheap In a quick break from our typical hacks and mods, learn to create a simple macro (close up) photography setup allowing you to create some fantastic, professional shots (see some samples below). Â�...
  • iPhone macro lens carousel iPhone macro lens carousel: " This iPhone macro lens carousel mod is a great way to recycle that pile of scavenged optics you've got laying around. [via LifeHacker]
  • 1
  • 2
  • 3
  • 4
  • 5