Biochip Printing using Virtual Instruments

Herbert Pichlik July, 7 2003

Fig. 1: TopSpot System

For its business activities involving biochip technology including the development, production, marketing and
application of biochips GeneScan Europe AG has coined the term BioChipnology. Biochip-based analysis
represents the most advanced method to analyse biomolecules, especially nucleic acids.
The surface of a biochip generally accommodates a few hundred to a few thousand spots (radius: 100 300 m)
with coupled biomolecules . These are created in the form of a matrix (microarray) using a printing system.
This special matrix of biomolecules forms the DNA array, the biochips sensitive core.
The advantages of biochip analysis lie in the synchronisation, miniaturisation and high speed of the entire
analytical process. This also entails a reduction in costs due to savings made on materials and reagents.
Moreover, biochip analysis boosts the efficiency and precision of the analytical process.
GeneScan Europe AG was among the first companies to move into the field of microarrays (microarray =
defined micro-arrangement of biomolecules in matrix form), which are often also referred to as DNA arrays or
biochips. In the microarray sector, GeneScan specialises in low and medium spot density biochips. Low-density
biochips include all those that accommodate between ten and several hundred different biomolecules. The
medium-density range can accommodate up to 10,000 different biomolecules functioning as information
carriers.
Biochip analysis is a highly innovative method of modern molecular biology. The core of this analytical
technology are biochips. These consist of a carrier, made of glass or other materials, on which biomolecules
are fixed in high numbers and densities in a defined microarray. Depending on the purpose of the test, the
surface can contain several hundred or several thousand spots with linked biomolecules. Each spot represents the
equivalent of a conventional analysis in a test tube. The matrix of spots applied to the biochip reproduces each of
these analyses several times up to a total of three or four and thus increases the reliability of the test result.
The advantages of biochip analysis compared to conventional analytical methods lie in the synchronisation,
miniaturisation and acceleration of the analytical process, and are also reflected in the material savings caused by
the minimisation of sample volumes and reagent use, along with an associated reduction in costs. Biochip
analysis considerably boosts the efficiency and measuring accuracy of the analytical process, and also brings
about greater flexibility and mobility. Depending on the density of the media applied to the carrier materials,
several thousand analyses can be accommodated on a single biochip.
Areas of application for biochip technology include the analysis of plant and animal genetic material, the
analysis of pathogens and infections, human genetic questions, gene activity studies and the investigation of

differences in DNA sequences. GeneScan develops, produces and markets biochips equipped with different
features, thus covering a wide range of areas including food and environmental analysis, medical diagnostics
and scientific research.
In biochip analysis, the key and lock principle of complementary hybridisation is utilised. Freely-moving
molecules from the test sample that are marked with a fluorescent dye (key) are brought into contact with
specifically designed and synthetically produced biological probe molecules (e.g. genetic material, DNA), which
are fixed to the carrier (lock). When the identical probe molecules of a spot match up with and capture their
complementary binding partners for the test feature from the analysis sample, the linked fluorescent dye is
likewise immobilised on the chip. The respective positive spot on the microarray lights up in the subsequent
detection reaction. Via hybridisation a specific molecule in the test sample (key) can be identified if it binds to
the complementary molecule (lock) which is immobilised on the chip in the form of a synthetic probe with a
defined structure.
The TopSpot printer is a patented, contact-free printing system for biomolecules. The printheads manufactured
by silicon micromachining technology permit simultaneous printing of 96 different media. Top-quality
microarrays can be produced because each printing module reproduces the whole array without mechanical
displacement and applying precise dosage volumes.
(fig. 5,6,9)

Fig. 2-4: Printing modules and print patterns

With the TopSpot system (TopSpot D) GeneScan, together with its partner SYSTEC GmbH (www.systecgmbh.com, Germany), have developed a model that has been specifically designed to meet the requirements for
high-throughput production of biochips.

Hardware
TopSpot D is a high speed and low cost microarrayer (fig. 1, fig. 2) that leverages latest PC and DAQ
technologies. All DAQ, IMAQ, signal conditioning, and motion components are located in a Coolermaster
aluminium PC case. The system features three power supplies (Enermax ATX power supply 430W, 24V DC/DC
converter, high voltage power supply). The Enermax device supplies the mainboard, plug in boards, drives, and
the motion controller with voltage.
The motherboard is a Pentium IV based ASUS P4C800 i875 Canterwood mainboard. The Intel 875P chipset is
Intels latest desktop chipset products to integrate the most advanced PC technologies available today, and to
boost the system performance to the next level through the state-of-the-art 800MHz front side bus.
Specs
CPU Intel Pentium 4 / Celeron / Prescott up to 3.6+ GHz
Intel Hyper-Threading Technology ready
Chipset Intel 875P MCH, Intel ICH5R
FSB 800/533/400 MHz
Memory Dual Channel DDR400, 4 DIMM Sockets, Max. 4GB
Expansion Slots 1 x AGP 8X, 5 x PCI
1 x ASUS WIFI connector for Wireless LAN upgrade
Storage ICH5R:
2 x ATA100, 2 x Serial ATA with RAID 0
Audio ADI AD1985 6-channel CODEC, Audio ESP
LAN 3COM 3C940 10/100/1000 Base-T, VCT
AI Features
AI Audio, AI NET, AI Overclocking
AI BIOS: CrashFree BIOS 2, Q-Fan, POST Reporter
The graphics subsystem is based on an ATI Radeon 9600 Pro chip with DVI interface that is directly connected
to a digital 17 TFT display with integrated speakers.
The piezo actuator is controlled via NI PCI 6711 High Speed Analog Output Card and an APEX high voltage
amplifier. The PCI 6711 and the APEX HV AMP (integrated in a 5,25 device bay) are connected together with
the SYSTEC I/O subsystem thats located in a 5,25 bay. Each liquid can be printed using different waveforms.
Upon activation of the actuator, droplets of the printing solution are ejected out of the nozzles. The droplet
volume is about 1nl and can be adjusted using different waveforms.

Fig. 5: Nozzles
All waveforms can be manipulated with an LabVIEW teaching subsystem. The waveforms and all relevant test
data are stored in a database. The customer can decide which database to chose.

channel for
pressure compensation
seal ring

cover plate

reservoirs

piezo-actuator
piston
cooling plate

nozzle array

supply channel from reservoir

Fig. 6: Print head schematics

The printing head together with a SONY firewire color camera DFW-SX900 and the programmable illumination
subsystem (SYSTEC I/O) is mounted on the z-axis of the microarrayer.
A new-age digital camera that produces never-before-seen levels of detailed, uncompressed images, Sony's
DFW-SX900 high-resolution color C-mount digital camera is in a league of its own. The camera incorporates a
1/2" Interline (IT) progressive scan 1.45 million-pixel CCD and includes an IEEE-1394 digital interface. A
compact and lightweight design makes the DFW-SX900 easy to install and ideal for a variety of quality critical
applications, such as machine vision, photo ID badging, microscopy, and high-resolution display.

The dropsizes are 100% verified via image acquisition using the NI IMAQ library. The camera is controlled by
LabVIEW VIs using the NI IEEE1394 driver. The NI-IMAQ based LabVIEW algorithms are responsible for
biochip analysis.

The air conditioning subsystem is essential to prevent the evaporation of the droplets. This subsystem is fully
controlled using a low budget NI 6014 DAQ device and the SYSTEC I/O subsystem.
The glass plates are positioned using a cross table with a movement range of (X,Y) 300 by 300 mm. The cross
table and the z axis are fully controlled using a Lang LSTEP system.

Fig. 7: Glass plate arrangement

The LANG LSTEP-PCI positioning system is a high-resolution stepping motor controller in the form of a PC
plug-in module for the PC. This device is used to control three axes with 2/4 phase stepping motors.

Fig. 8: LANG LSTEP-PCI positioning system

Communication between the PC and the controller takes place through the PCI bus topped by a Dual-Port Ram.
Dynamic micro step operations allow positioning operations to be done quickly and with the highest precision.
The integration of a controller and power amplifiers on a plug-in device for the PC provides compact, EMCcompliant systems without additional mechanical requirements. This solution is ideal for applications where cost
is a sensitive factor. A wide range of equipment options provides more flexibility, allowing to adapt the system
to meet individual needs.
The price performance ratio is excellent because of the lack of an external chassis with implemented power
amplifiers.

Software
LabVIEW is the ideal platform for integrating different Virtual Instruments in one application. LabVIEW 7
Express marks a new milestone in Graphical Dataflow Programming. The TopSpot software utilizes new
features of LabVIEW 7 Express, especially dynamic event management.
Together with a message based and event controlled state machine the TopSpot application only uses some
percent CPU power. The hole application has NO local variables. The DAQ devices are controlled using the
traditional DAQ library (the new DAQmx environment does not support all NI hardware components used by
now).
The system is extremely robust because the WindowsXP explorer shell is replaced by the TopSpot application.
System procedures that are not required are not started.

fig. 9:

Front panel

fig. 10 Part of block diagram (main VI)

The user interface was developed using sophisticated SYSTEC ergonomic guidelines. All relevant informations
are visible on one tab control instance. 70 percent of the VIs take care of plausibility checks and error
management. The Webworks help subsystem uses SYSTECs unique Video To Web software introducing
unrivalled text to speech technologies. The user interface supports multiple languages.
It is essential to define software standards for each project. As TopSpot is a product that is distributed worldwide
the quality of the software and hardware components is in the center of interest.
The TopSpot software development plan is based on a waterfall development model. The waterfall model is the
classic model of software engineering. It has deficiencies, but it serves as a baseline for many other lifecycle
models. The pure waterfall lifecycle consists of several non-overlapping stages. It begins with the software
concept and continues through requirements analysis, architectural design, detailed design, coding, testing, and
maintenance.

The software requirement standards (SRS) are based on GPP (good programming practice) standards of the
LabVIEW Usergroup Central Europe e.V. (internal Draft).
Basic thoughts of Gradys and Caswells FURPS (Functionality, Usability, Reliability, Performance, and
Supportabilty) model [6] are implemented in this model.
Metrics are defined to deal with following FURPS items:

Functionality
o

Feature set

Capabilities

Generality

Security

Usability
o

Human factors

Aesthetics

Consistency

Documentation

Reliability
o

Frequency/severity of failure

Recoverability

Predictability

Accuracy

Mean time of failure

Performance
o

Speed

Efficiency

Resource consumption

Throughput

Response time

Supportability/Maintainability
o

Testability

Extensibility

Adaptability

Compatibility

Servicability

Installability

o Localizability
Conclusion
TopSpot D is a LabVIEW based contact-free printing system for biomolecules. The system is easy to use,
extremely cost effective, and very fast. Incorporating the latest hard and software technologies leads to
unrivalled productivity.

The author
Herbert Pichlik was born in 1958; he studied electrical engineering at the Georg-Simon-Ohm University of
Applied Sciences in Nuremberg. He started his professional career in 1985 when he joined Philips
Kommunikations Industrie AG (PKI) as a software development engineer. Later, he moved to the quality
management department at PKI. After a short period at LGA, he joined Quelle AG in 1990, where he has been in
charge of measuring and test instrument management as well as test instrument development. After being
product manager at Testware he joined SYSTEC GmbH in mid 2000 as manager of the test and automation
division.
Herbert Pichlik has written and coauthored several books and dozens of papers and articles. Since 1992, when he
assumed responsibility for a large number of different projects, he has worked intensively with LabVIEW.
Herbert Pichlik is an internationally awarded synergist, enthusiastic squash player, father of four children, and
owner of several patents in the field of analog and digital integrated circuit technologies; he started lecturing in
graphical data flow programming at the Nuremberg University as a sideline in 1997. Since 2002 he is president
of the LabVIEW Usergroup Central Europe e.V. (www.lvug.de)

References
[1]
Herbert Pichlik, Universal Test- and Automation System using an event driven object oriented
LabVIEW approach (UTAS), NI-Week 2001 Proceedings, Austin TX 8/01
[2]
Herbert Pichlik, G++ New Directions in Information Technology, NI-Week 2001 Proceedings, Austin
TX 8/01
[3]
Rahman Jamal, Herbert Pichlik, LabVIEW Applications and Solutions, Prentice Hall 8/98
[4]
Herbert Pichlik, Universal testing of household equipment using LabVIEW,
Best applications of virtual instrumentation, NI-Week 96 Proceedings, Austin TX 8/96
[5]
Herbert Pichlik, Networkcentric test and measurement system,
Best applications of virtual instrumentation, NI-Week 97 Proceedings, Austin TX 8/97
[6]
R. Grady and D. Caswell, Software Metrics: Establishing a Company-Wide Program, Prentice Hall,
1987.
[7]
www.ni.com/labview
[8]
www.lang.de
[9]
www.gooptech.com
[10]
www.lvug.de
[11]
www.systec-gmbh.com
[12]
www.genescan.com
[13]
www.apexmicrotech.com
[14]
www.asus,com
[15]
www.sony.com

Herbert Pichlik
Badener Str. 44
D-90518 Altdorf
Germany
Phone 0049-9187-903276
Fax
0049-9187-903278
[email protected]