„A” Sub-project Report

1. Identification

Registration No. of the application A/CZ0046/1/0008
Number of the Grant Contract A/CZ0046/1/0008
RF(CZ) Sub-project Report Interim report         Number: 2
Report submitted to Intermediary 12.11.2009 09:28
Accepted by the Intermediary 18.11.2009
Starting date of the sub-project 01.11.2008 Closing date of the sub-project 30.04.2010 Duration of the sub-project 18
Full name of the sub-project Integrated tools and models for high-throughput and high-content analyses in food safety and quality - HCTFOOD
Priority sector R&D in food safety and quality


Legal name of the final beneficiary Jihočeská univerzita v Českých Budějovicích
Address Branišovská 31,
370 05 České Budějovice
Czech Republic
Postal address
if differs
Ústav fyzikální biologie
Institute of Physical Biology
Zámek 136
373 33 Nové Hrady
Czech Republic
Legal representative(s) prof. PhDr. Václav Bůžek CSc., Doc. RNDr. Dalibor Štys CSc.
Position rector, director of the Institute of Physical Biology
Contact person Doc. RNDr. Dalibor Štys CSc.
Phone +420 389 033 802 E-mail stys@jcu.cz
Skype Web pages http://www.bieng.over.cz/

2. Activity report / changes

Describe in brief how all appropriate activities from the application were done according agreed time-schedule. Explain role of the partners, relevant expenditures, mention events organised and attended, publicity, results and outputs.
If no action appears in activity or actions were in delay, explain it.
Multivariate dynamic modelling of biological systems
Description This activity is led by Norwegian partner A and partner B.

Activity Pre-processing of data for noise reduction, normalization and removal of systematic but undesired variations of ESMC

Hyper-spectral FTIR microscopy images of individual cells have been analyzed for two types of cell lines, in cooperation with an Englis and a US university. A cell line of human liver cells has been established at Nofima and monitored successfully as a function of growth conditions by FTIR biospectroscopy. A Raman confocal microscope for in vivo monitoring of cells has been installed and is now being tested.

In preparation for the microscopy monitoring of living cells, various software tools are being developed, as part of other projects and activities. A series of new proteomics data based on 2D poly-acrylamide gels have been successfully prepared at Nofima Mat AS according to a conscious statistical design at Nofima Mat AS, including a number of time-evolution image sequences of protein gel staining. Work is now in progress to analyze and publish these data. Part of this work is done by a PhD student based on other funding, and part of it is done by the Nofima scientists within this EEA project, as planned. Moreover, we have successfully tested our new pixel-based software for data modeling of a series of 2D gel electrophoresis proteomics images, in cooperation with Norwegian University of Science and Technology, Trondheim, and with a Polish university.

Impact to project budget
The budget was spent as expected.

Presentation of results:
Project web page is www.bieng.over.cz/project.htm. Unfortunately due to applied character of the project, the result could not be published until the intellectual property protection is clarified. This is expected to be for all software packages by the end of November 2009.

Activities multivariate analysis of pre-processed data, attempts to rotate latent variables, Attempts to estimate local structure
Experiments proceed according to the plan. Time is too short for conclusive reportable results.
Changes No changes
Scientific meeting and joint education activities
Description This activity is organized jointly by both partners

Second project meeting is scheduled to July 2009 in Nové Hrady
Second course “Physical biology” was held in Nové Hrady on May 18 – 22 and June 1 - 12. , 2009
By this, the proposed number of activities is fulfilled.

Besides that, from the project budget was supported also the presentation o results at 10th International Conference "Pattern Recognition and Information Processing";2009, Minsk and at 3rd FEBS Advanced Lecture Course on Systems Biology from Molecules to Function, Alpbach, March 7.-13th 2009.

Impact to project budget
Due to progress in project activities, the increase of the share of travel costs in the project budget is requested.
Changes No changes
Experimental tools for multivariate description in microbiology and cell biology
Description This activity is led by the Recipient.
Activities Metabolomic analytical tools development and Analytical tools and instrument drivers for microscopic time lapse experiments.
Succesfull implementation of software packages was reported in period 1 (month 1-3). These packages are publicly available at www.bieng.over.cz. Publication of these results must be constrained before the publication and implementation to industrial since these have to be done in conformity of the publication policy of the appropriate journal, proceeding publisher or needs of the partner.

Research and development results:
Recipient negotiated the implementation with the user, company BP Medical and it was agreed to publish the results in international journal to prevent eventual creation of software patent. Software patents are possible in USA, in Europe these are possible only as part of the instrument patent. Both packages have the character of instrument applications and may be easily patented also under European law. The user is not a producer of instruments and the software patent is not an option, we thus decided to control the priority by publishing and presentation.

We submitted following journal papers:
Expertomica Metabolite Profiling: Getting more information from LC-MS using the stochastic systems approach, Bioinformatics, published online July 14th, 2009 – relevant to software package Expertomica Metabolite Profiling
Expertomica Cells: Analysis of cell monolayer development Bioinformatics under revision – relevant to software package Expertomica Hela Cells 3.03 RC.

And presented following papers in indexed conference proceedings:
Preprocessing of microscopy images via Shannon's entropy, 10th International Conference "Pattern Recognition and Information Processing";2009, Minsk, ISBN 978-985-476-704-8 – relevant to software package Expertomica Compute Entropy on GPU toolbox
Preprocessing of microscopy images, via Shannon's entropy on GPU, GraVisMa (Computer Graphics, Computer Vision and Mathematics), Plzen, September 2009 Pilsen, indexed proceedings due to be published in November 2009 – relevant to software package Expertomica Compute Entropy on GPU toolbox
Maximisation of image contrast in label-free microscopy of living cells using information entropy computation, CYTOKINEMATICS 2009, Microscopy of Live Cells in the Post Genomics Era, The 11th symposium on live cell imaging, Hradec Kralove, ISBN 978-80-7399-816-5 - – relevant to software package Expertomica Compute Entropy on GPU toolbox
Expertomica metabolomics profiling: Using probabilistic system approach to gather more information from LC-MS, SIMONA 2009 Liberec, Indexed proceedings due December 2009 – relevant to software package Expertomica Metabolite Profiling
Entropy fluxes in cell culture and its parallel implementation on GPU, SIMONA 2009 Liberec, Indexed proceedings due December 2009 – relevant to software package Expertomica Compute Entropy on GPU toolbox
RGB channels (in)dependence in phase contrast microphotography, Technical Computing Prague 2009, 19.listopadu, Indexed proceedings due Nov. 2009 – relevant to software package Expertomica Compute Entropy on GPU toolbox

Impact to project budget:
We decide to present the software package Expertomica Compute Entropy on GPU toolbox at the conference and publish it in a conference proceeding since the included method has broader impact including theoretical consideration. The peer reviewed paper, after complete theoretical analysis, may reach prominent journal (as suggested by partner A and partner B). We sought the cheapest way for such presentation and among the image processing conferences in 2009 we selected 10th International Conference "Pattern Recognition and Information Processing";2009, Minsk. The alternatives were Canada and China.
Otherwise the budget was spent as expected.

Presentation of results:
Project web page is bieng.over.cz/project.htm. Unfortunately due to applied character of the project, the result could not be published until the intellectual property protection is clarified. This is expected to be for all software packages by the end of November 2009.

Activity Microscopic characterisation of cells with different genetics, at different stages and environment
Experiments proceed according to the plan. Time is too short for conclusive reportable results.




Changes No changes
Project management
Description Project indicators were fulfilled as follows:
1) Number of publications of results in prestigious journals (impacted, indexed or reviewed):4 (planned), 8 (realization in 1st period), 2(realization in 2nd period), 10 (cumulative)
2) Number of organizations supported (applicant and partners): 3 (planned), 3(realization in 1st period), 3 (realization in 2nd period), 3 (cumulative)
3) Number of R&D events supported (active participation at public seminars, conferences, exhibitions): 2 (planned), 2(realization in 1st period), 4(realization in 2nd period), 6 (cumulative)
4) Implemented software packages:2 (planned), 4 (realization in 1st period), 0 (realization in 2nd period), 4 (cumulative)
5) Number of new grants / contract of partnerships between the Czech Republic and EEA EFTA countries: 2(planned), 1(realization in 1st period), 1 (realization in 2nd period), 2 (cumulative)
6) Number of products (e.g. methods, procedures, technologies) transferred (planned transfers): 2 (planned), 4 (realization in 1st period), 0 (realization in 2nd period), 4 (cumulative)
7) Number of new patents, prototypes and/or industrial applications: 2 (planned), 0 (realization in 1st period), 1 (realization in 2nd period), 1 (cumulative)
8) Project meetings: 2 (planned), 1 (realization in 1st period), 0 (realization in 2nd period), 1 (cumulative)
9) Courses: 2 (planned), 1 (realization in 1st period),1 (realization in 2nd period), 2 (cumulative)


Results (planned/current situation), outputs:
1) Number of publications of results in prestigious journals (impacted, indexed or reviewed)

Impacted journals:
Expertomica Metabolite Profiling: Getting more information from LC-MS using the stochastic systems approach, Bioinformatics, published online July 14th, 2009
Singular perturbation based solution to optimal microalgal growth problem and its infinite time horizon analysis, accepted with revisions to IEEE Trans Aut. Contr.
Expertomica Cells: Analysis of cell monolayer development Bioinformatics under revision
Conference contributions with reviewed papers:
Maximisation of image contrast in label-free microscopy of living cells using information entropy computation and objective definition of cell state, Super and High Resolution Imaging Conference, Lipica, Conference papers will be published in special issue of Micron early 2010
Parallel stochastic simulation of the cell culture growth in a bioreactor, HiBi Trento 2009, conference paper will be published in International Journal of Advanced Science and Technology or to the International Journal of Bio-Science
and Bio-Technology
Conference contributions with papers in indexed proceedings:
Preprocessing of microscopy images via Shannon's entropy, 10th International Conference "Pattern Recognition and Information Processing";2009, Minsk, ISBN 978-985-476-704-8
Preprocessing of microscopy images, via Shannon's entropy on GPU, GraVisMa (Computer Graphics, Computer Vision and Mathematics), Plzen, September 2009 Pilsen, indexed proceedings die to be published in November 2009
Maximisation of image contrast in label-free microscopy of living cells using information entropy computation, CYTOKINEMATICS 2009, Microscopy of Live Cells in the Post Genomics Era, The 11th symposium on live cell
imaging, Hradec Kralove, ISBN 978-80-7399-816-5
Expertomica metabolomics profiling: Using probabilistic system approach to gather more information from LC-MS, SIMONA 2009 Liberec, Indexed proceedings due December 2009
Entropy fluxes in cell culture and its parallel implementation on GPU, SIMONA 2009 Liberec, Indexed proceedings due December 2009
RGB channels (in)dependence in phase contrast microphotography, Technical Computing Prague 2009, 19.listopadu, Indexed proceedings due Nov. 2009
4 (planned) 8 (realization in 1st period) 2 (realization in 2nd period)

2 ) Number of organizations supported (applicant and partners)
The three organisations which applied for the grant are supported Institute of Physcial Biology,Nofima and Cigene. 3 (planned), 3 (realization in 1st period), 3 (realization in 2nd period)

3) Number of R&D events supported (active participation at public seminars, conferences, exhibitions)
Period 1: R&D events supported:
Prof. Stys participated at ICT Europe in Lyon (co-supported by Europen commsion) and at the Pollutech in Lyon (co-supported by Czech Ministery of Industry and Trade).

Period 2:
J. Urban and D. Štys participated at
3rd FEBS Advanced Lecture Course on Systems Biology: From Molecular Biology to Biological Function and
J. Urban, T. Levitner, Š. Papáček, J. Vaněk and D. Štys participated at 7th meeting of Czech Structural Molecular Biologists in Nové Hrady
J. Urban and, J. Vaněk 10th International Conference "Pattern Recognition and Information Processing";2009, Minsk
J. Urban, T. Levitner and D. Štys participated at series of events in ISTA Klosterneuburg (Austria):
3 June: 09:30 – 15:00: Scientific Symposium “The Human Brain as the Most Powerful Computer”
3 June: 16:00 – 19:00: Panel discussion with leaders of international world class research institutions: “Institutes of Basic Research: Is There One Formula for Success?”
3 June: 20:00 – 22:00: Panel discussion with leading personalities from industry “From Basic Research to Economic Value”
4 June: 09:00 – 15:30: Scientific Symposium “Neurons and Machines”
2 (planned), 2 (realization in 1st period), 4 (realization in 2nd period)

4) Implemented software packages
Period 1:
There have been prepared four software tools relevant to the project. In preparation is their final placement at the website. The softwares are:

i) Expertomica Metabolite Profiling

Program for LC/GC-MS measurement analysis. It works with text records of the measurement in Agilent ASCII, Thermo ASCII and JCAMP-DX ASCII formats. It performs filtration of random and systematic noise, peak detection and compound composition on the basis of probability theory. It enables visualization by graphs of detected peaks as well as noise parts.

ii) Expertomica Time-Lapse Microscopy Capture Tool

Program for capture of microscope images. It is designed for capturing of long image series, more detailed analysis of information content and processes occurring in the microscopy sample. In comparison to classical software tools, it has better possibilities in exposition setup, possibility to capture images with several camera setup at one time. One of typical applications is the possibility to capture several images with different exposition time and in this way to overcome the dynamic limit of camera. In the current version Olympus cameras are supported.

iii) Expertomica Compute Entropy on GPU toolbox

Program for computation of informations content of individual pixels in one digitized image or between two images. It serves as one of the methods for image processing during automated image analysis. It is based on calculation of Shannon entropy for all combinations of lines and rows. This calculation is highly computationally intensive and this toolbox was developed to accelerate the original Matlab calculation using nVidia graphic cards. It reduces the computation time thousand times. In the case that the graphical card is not present in the computer, the computation is performed on the CPU in optimized C++ version of algorithm. The program is primarily developed for analysis of images captured by the phase contrast microscopy method. It can be utilized for any intensity (black and white or pseudo-RGB) images.

iv) Expertomica Hela Cells 3.03 RC

Program for creation of computer description of cell culture development in time lapse microscopy. EHC is primarily developed for description of He-La cells with the experiment size of up to 1500 analysed images and 30-50 cells per image. With certain restrictions it may be used for bigger experiments and other types of cells.
EHC is written in Java which ensures almost non-restricted compatibility for all platforms and operation systems. The advantage is also small size of the program.

Period 2:
Only software testing and development was performed in this period, 4 new packages are due in period 3

In this way, the goals of the project were twice exceeded
2 (planned), 4 (realization in 1st period), 0 (realization in 2nd period)

5) Number of new grants / contract of partnerships between the Czech Republic and EEA EFTA countries
Period 1:
Grant application “Entropy based complex stochastic systems state and behaviour analysis and prediction for biomedicine and biotechnology entrobio“ was jointly supported to the EU FET Open 2007 call of the FP7 program of EU.
Period 2
Application: Engineering approach to biological information processing was submitted to EU FET Proactive call.
2 (planned), 1 (realization in 1st period), 1 (realization in 2nd period)

6) Number of products (e.g. methods, procedures, technologies) transferred (planned transfers)
Period 1
Among the softwares prepared, all are meant for practical use in food and biomedical practice. They may be considered new methods.
Period 2
No new transfers
2 (planned), 4 (realization in 1st period), 0 (realization in 2nd period)

7) Number of new patents, prototypes and/or industrial applications
Period 1:
The implementation of the new methods to practice makes the industrial application. We collaborate with companies in the science park to implement the software packages in practice of biotechnology and food technology. Both sides shall supply real life data from food industry to test the technologies developed, namely the LC-MS data and time-lapse microscopy data.
Sofware package Expertomica cells became used in experimental practice of the company BP Medical.
Period 2
New prototype of the bioreactor utilizing Couette-Taylor mixing was constructed and extensively tested in July 2009
2 (planned), 0 (realization in 1st period), 1 (realization in 2nd period)

8) Project meetings
Period 1
First project meeting was held at January 13, 2009 in As.
Period 2: no project meetings
Project meeting is scheduled to July 2009 in Nové Hrady
2 (planned), 1 (realization in 1st period), 0 (realization in 2nd period)

9) Courses
Period 1
First course was the “Multivariate data modeling in systems biology” which was held at January 12-16 2009 in As.
Period 2
Second course “Physical biology” was held in Nové Hrady on May 18 – 22 and June 1 - 12. , 2009
2 (planned), 1 (realization in 1st period), 1 (realization in 2nd period)

Changes No changes
Practical pilot assessment in selected advanced food products
Description No activities were planned for reported period
Changes No changes

3. Financial report

3.1. Sub-project expenditures and payments overview Total sub-project costs Grant % of total costs Advance payment % of grant
Grant contract 127458 111118 87.18 55559 50
Report Reported expenditures Rejected expenditures Approved expenditures Payment request Payment order
sum % of total sum % of grant
1st interim report1429301429311.21---
2nd interim report1930501930515.15168301683015.15
Final Balance     33598 26.36   72389 65.15
Not used     93860 73.64   38729 34.85

3.2. Remarks to Financial report

Project spendings on the side of the recipient proceeded according to plan. Partner A
and partner B delayed spending due to unclarities in project funding. Partners A and B did not want to
spend money on their side until it was clear that the report for period 1 is accepted.
And that happened only at 5th of August 2009.

Co-financing of the 16340 EUR (12,82% of the total eligible costs for the sub-project) is provided by own financial resources of the Institute of Physical Biology of the University of South Bohemia in Česke Budějovice. We have filled an application to the Ministry of Education, Youth and Sports on 15th of September 2009 in the 6th phase for the financing of the institutional co-financing of international projects. In case of granting the requested support we shall use this fund to co-finance the project instead of the former resources.

4. Procurement

Describe in brief all tenders for goods and services with predicted value of €5.000, excl. VAT, and above for the sub-project. Describe their criteria, evaluation, date of the contract signature, total price, delivery and payment conditions.
No procurement has been planned for reported period.

5. External monitoring, control, audit, etc

Describe in brief all external monitoring visits, control, audit etc. connected (even partially) to the sub-project. Describe their conclusions, adopted corrective measures, fines awarded etc.
No external monitoring, control, audit..etc. has been planned for reported period

6. Attachments

Please enclose to the report: (Time sheets neednot to be enclosed to the report)
Form 3.3
Breakdown of Expenditures
/data/zpravy-a/29-1-Breakdown_vypisy.zip
Form 3.4
Budget Changes
N/A