„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: 1
Report submitted to Intermediary 05.08.2009 12:43
Accepted by the Intermediary 05.08.2009
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 www.greentech.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 There was prepared (Insitute of Physical Biology) and published at the web page http://www.bieng.over.cz/software.html a software tools, namely Expertomica Metabolite Profiling,. The performance of the Expertomica Metabolite Profiling toolbox was successfully tested on data obtained in NOFIMA Food laboratories. Results of the analysis were also successfully analysed by multivariate analysis methods developed at NOFIMA Food and Cigene. Both results are preliminary yet this part of the project is running ahead of time.
Changes There will be need for more direct contact joint work. Corresponding change in the project financial plan were requested
Scientific meeting and joint education activities
Description The first project meeting was organized in As at January 13th and continued at January 14th and 15th, 2009. 3 persons from Insitute of Physical Biology participated in the course Multivariate Data modelling for systems biology in As at January 12th – January 16th 2009. This part of the project is running ahead of time.

Indicator
Number of publications of results in prestigious journals (impacted, indexed or reviewed):
8 articles were submitted to impacted peer review journals. First article is under revision in Bioiformatics, other are in review process. Planned: 4 Realization: 8

Number of organizations supported (applicant and partners):
The three organisations which applied for the grant are supported: Ústav fyzikální biologie Institute of Physical Biology Zámek 136 373 33 Nové Hrady Czech Republic, Matforsk AS - Osloveien 1 - N-1430 Ås - Norway, CIGENE, Norwegian U. of Life Sciences,N-1432 Aas, Norway
Planned:3 Realization: 3

Number of R&D events supported (active participation at public seminars, conferences, exhibitions) :
R&D events supported:Czech partners informed on their planned participation at the The 3rd FEBS Advanced Lecture Course on Systems Biology: From Molecular Biology to Biological Function and at the 7th meeting of Czech Structural Molecular Biologists in Nové Hrady. Prof. Stys also 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). By this, the numerical value of this criterion is twice exceeded, however, attention to other meetings will be co-supported by HTCFOOD.
Planned: 2 Realization: 4

Implemented software packages:
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.

In this way, the goals of the program were twice exceeded.
Planned: 2 Realization:4

Number of new grants / contract of partnerships between the Czech Republic and EEA EFTA countries:
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. Similar application, extending the problem from the point of view or realism of interpretation of information processing in biology by the common perception of information sciences will be submitted to EU FET Proactive call. Other deadlines will be followed and applications submitted.
This part of the project has been fulfilled by 50%. Planned:2 Realization:1

Number of products (e.g. methods, procedures, technologies) transferred(planned transfers):
Among the softwares prepared, all are meant for practical use in food and biomedical practice. They may be considered new methods. We believe that the category software packages and new technologies overlap and has been fulfilled.
Planned:2 Realization:4

Number of new patents, prototypes and/or industrial applications:
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.
Planned:2 Realization:0

Project meetings:
First project meeting was held at January 13, 2009 in As. Next meeting is planned to May/June 2009 in Nové Hrady
Planned:2 Realization:1

Courses:
First course was the “Multivariate data modeling in systems biology” which was held at January 12-16 2009 in As. Second course will be “Physical biology” to be held in Nové Hrady on May 18 – 22 and June 1 - 12. , 2009
Planned:2 Realization:1








Changes No changes

Experimental tools for multivariate description in microbiology and cell biology
Description There were prepared software tools Expertomica Time-Lapse Microscopy Capture Tool, Expertomica Compute Entropy on GPU toolbox, Expertomica Hela Cells 3.03 RC. These tools will be extended for macroscopic imaging of cell cultures by near infrared and to time evolution of protein gel staining. This part of the project proceeds according to expectations.
Changes No changes
Project management
Description First project management meeting was held in As at January 14th and continued at January 15th. Present were all project leaders, Dalibor Stys, Harald Martens and Ellen Mosleth Faergestad. There was discussed project progress and project partnership agreement. Small changes were suggested by Nordic partners and are now implemented. Project management progresses cording to the plan.
Changes No changes
Practical pilot assessment in selected advanced food products
Description No work was planned in this task in 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---
Final Balance     14293 11.21   55559 50
Not used     113165 88.79   55559 50

3.2. Remarks to Financial report

In this project we originally planned one visit of coordinators to the partner’s workplace in As and the support of conference’s participation. During the visit in As it turned out, that longer visit and implementation of developments software instruments are required. For this reason we require a larger sum of travel costs. On the other hand, many of the software tools were provided in advance and have allowed for substantial savings in the consumables and running costs budget categories. We request to use the latter to increase the travel costs budget.

Příjemce je vykázal za 1.- 3.měsíc realizace subprojektu čerpání ve výši 12,49 % z hodnoty grantu,což je poněkud méně, než odpovídá časovému průběhu subprojektu (3 měsíce/18 měsíců =16,7%)- žádáme o stručný vysvětlující komentář v této části zprávy:
Delayed utilisation of project funds, namely at Norwegian side, was caused by unexpectedly long negotiation of the partnership contract. Both sides had to agree on method of accounting and activity declaration which would be valid for all acounting systems and rules included. In the period preceeding and following the Chrismas and New
Year, many resposnible persons were not mutually present which delayed the communication. This fact did not have impact on project activities.

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 tenders were planned.

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 audit was planned.

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/13-1-Expenditure breakdown a vypisy.zip
Form 3.4
Budget Changes
/data/zpravy-a/13-2-budget changes.xls