Center for Biosystems

Center for Information Technologies

Project aim: Bioaerosols are among the most complex components of the atmosphere, important pathogens in crops and on trees, and aeroallergens. The overall goal of the BREATHE project is to set the foundation for IT-based real-time atmospheric diagnostics in Serbia by advancing the use of flow cytometry in aerobiological research.
&nbsp;
About the project: Real-Time Airborne Particle Identiﬁer (Rapid-E) is designed for real-time sampling and analysis of airborne particles and produces light scattering, fluorescence spectrum and the lifetime of fluorescence signals of detected aerosols. Dealing with such a huge amount and diversity of data makes Artificial Intelligence method of choice for analysis. BREATHE will analyse the variability of fluorescence emission for chosen bioaerosols of different age and humidity levels in parallel by using Rapid-E flow cytometer and spectrofluorometer. It will explore the application of novel image processing algorithms for reconstructing a representation of particle morphology based on light scattering. The project will use Artificial Intelligence and data science methods to build a machine learning-based classification model for bioaerosols and deliver the result in real-time. Also, methods for unveiling black-box models will provide relevance scores indicating the most discriminative features. This will allow better classifications by the involvement of domain knowledge in primarily data-driven models. Application of transfer learning concept is expected to improve generalization of the classification models and thus their use on different measurement devices. The results of the research will provide great potential to reinforce the leading position of the Republic of Serbia in the area of aerobiology and atmospheric diagnostics.
&nbsp;
The implementation of the BREATHE project will serve as the pilot on how a group for modern atmospheric diagnostics, combining researchers from the field of aerobiology, physics, chemistry and data analytics, should work together.
&nbsp;
&nbsp;
<img decoding="async" loading="lazy" class="alignnone size-medium wp-image-1391" src="https://api.biosens.rs/wp-content/uploads/2021/06/Logo-ENG-2-300x97.png" alt="" width="300" height="97" srcset="https://api.biosens.rs/wp-content/uploads/2021/06/Logo-ENG-2-300x97.png 300w, https://api.biosens.rs/wp-content/uploads/2021/06/Logo-ENG-2.png 512w" sizes="(max-width: 300px) 100vw, 300px" />

Principal Research Fellow 

Branko Šikoparija

Sanja Brdar is a senior researcher and head of the Centre for Information Technologies at BioSense Institute. She received a PhD degree from the University of Novi Sad in 2016. Prior to starting her PhD studies, she spent two years working in the software industry with a major in databases design and development. In 2010 she was awarded a ten-month Basileus fellowship for joining the Bioinformatics Laboratory at University of Ljubljana which set the foundations for the PhD thesis on data/knowledge fusion in bioinformatics. Currently, she is actively involved in many projects including H2020 Antares, Dragon, Bestmap and Flexigrobots and teaches two master level courses at Faculty of Sciences. Her research interests include machine learning, explainable AI and bioinformatics. She works on ensemble methods, data fusion, clustering, and predictive modelling with applications in biology, agriculture, environmental sciences and health. She enjoys participating in worldwide data science challenges and with the team of researchers made significant results: placed third in Nokia Mobile Data Challenge (2012), finalist of Orange, France, Data for Development Challenge (2013), finalist/winner/third place of Syngenta Crop Challenge (2016, 2017, 2019) and finalist of UNDP Depopulation challenge (2020).

Sanja Brdar

Dr. Marko Panić is a research associate in the field of technical sciences and information technologies at the BioSense Institute. His doctoral dissertation is related to the development of algorithms for accelerated image reconstruction from incomplete measurements using a sparse representation of signals and statistical Markov random models. His research direction includes statistical modeling of multidimensional data obtained from different sensors. He is currently working on the analysis and processing of images obtained from hyperspectral and multispectral cameras using advanced machine learning methods with application in assessing the quality of fruits and vegetables. As a member of the BioSense team, he participated in Syngenta's "Crop Challenge" competition, which resulted in winning first place. He is actively involved in many projects from the Horizon 2020 call, including Antares, Cybele, Dragon and Flexirobots, as well as in projects with companies such as Krivaja, MK Agri and Delta Agrar.

Marko Panić

Gordan Mimić is a research associate at Biosense Institute. Gordan Mimić received BSc (2011), MSc (2012) and PhD (2016) degrees in Physics-Meteorology at the University of Novi Sad, Faculty of Sciences. He was working at Republic Hydrometeorological Service of Serbia during the period 2011-2012, in the division for Numerical Weather Prediction. Gordan Mimić was teaching assistant for the various courses in meteorology at the University of Novi Sad (Faculty of Sciences and Faculty of Agriculture) in the period 2012-2017. His current research interest is data analytics in the field of agrometeorology and biometeorology. He was the leader of the BioSense team that developed a novel algorithm for the classification of maize hybrids tolerant to drought and heat stress, which won the third prize at Syngenta Crop Challenge in Analytics 2019. He participated in several national and international projects. Gordan Mimić has co-authored 20 journal articles, 4 conference papers and 1 book chapter.

Gordan Mimić

Dr Branko Sikoparija is a Principal Research Fellow at the Center for Biosystems and quality manager (ISO17025) in the Laboratory for Palynology University of Novi Sad Faculty of Sciences. His research focus is aerobiology and currently, he is interested in developing real-time detection and identification of bioaerosols. Branko Sikoparija is an accomplished writer and reviewer for multiple scientific research journals. Serves as Associate Editor for Aerobiologia. He coordinates the RealForAll network of automated bioaerosol monitors on the Pannonian plain. He is also an active member of the EUMETNET AutoPollen program, vice chair of the COST Action CA18226, the chair of the European Aerobiology Society Working Group for Quality Control, and principal investigator in the BREATHE project financed in the PROMIS call Science Fund of the Republic of Serbia.

&nbsp;

National

<img class="alignnone wp-image-1230 size-large" src="https://api.biosens.rs/wp-content/uploads/2021/06/campaigns-1024x401.jpg" alt="" width="1024" height="401" />

&nbsp;

We study the diversity of bioaerosols so as the processes involved in the emission and dispersion of particles of biological origin in the atmosphere. By focusing on airborne pollen and fungal spores, we set the foundation for modelling of aerobiological phenomena and forecasting their impact.

&nbsp;

The group started to study pollen in 1989 focusing on feeding habits of insects, in particularly honeybees and hoverflies.  We supported the local Association of beekeepers “Dr Jovan Živanovic” to register the protected designation of origin for “Fruška gora lime tree honey”. Since 1999 the research was oriented towards the agents of allergies when the group started continuous sampling bioaerosols by using Hirst type volumetric pollen and spore traps.

&nbsp;

In the BioSense Institute, classical aerobiology has the chance to utilise advanced IT tools both for sampling and detection of bioaerosols and for data analytics. We are striving to set the basis for source-oriented modelling of airborne pollen concentrations. Therefore, we are coupling remote sensing data and airborne pollen data to map sources of the most important allergenic pollen, and setting field experiments to parametrize emission of the pollen.

&nbsp;

Our group is also exploring the possibilities for using flow cytometry in automated detection and quantification of bioaerosols (i.e. pollen and fungal spores). We are also developing an automated pollen monitoring system and compare its performance with classical Hirst trap and microscopy-based method.

&nbsp;

We host an hourly resolved long term collection of air samples from typical agriculture region. In addition, we have reference signals of scattering, fluorescence spectrum and fluorescence lifetime collected by RAPID-e device for the majority of airborne pollen.

&nbsp;

Projects:

&nbsp;

2017-2020 “Real-time measurements and forecasting for successful prevention and management of seasonal allergies in Croatia-Serbia cross-border region” – <a href="http://www.realforall.com">RealForAll</a>, INTERREG IPA-CBC Croatia Serbia

&nbsp;

2020-2022 “Real-time detection and quantification of bioaerosols relevant for human and plant health” – <a href="https://www.realforall.com/language/en/project-breathe/">BREATHE</a>, Fond za nauku Republike Srbije

&nbsp;

2016-2020 Monitoring polena u vazduhu na teritoriji AP Vojvodine, Pokrajinski sekretarijat za zaštitu životne sredine

Aerobiology and palynology

BREATHE – Real-time detection and quantification of bioaerosols relevant for human and plant health

Centar za Biosisteme

Centar za Informacione Tehnologije

Cilj projekta: Bioaerosoli spadaju među najsloženije sastojke atmosfere. Monogi su važni patogeni biljaka ili alergeni. Postavljanje osnove za naprednu dijagnostiku atmosfere u realnom vremenu, u Srbiji je glavni cilj projekta. Projekat će primenom informacionih tehnologija, unaprediti upotreb protočne citometrije u aerobiološkim istraživanjima.
&nbsp;
O projektu: Uređaj Rapid-E je napravljen za uzorkovanje i analizu suspendovanih čestica u vazduhu, u realnom vremenu, i beleži podatke o rasejavanju svetlosti, spektre fluorescencije i vreme života signala fluorescencije. Međutim, rad sa velikom količinom različitih podataka zahteva izbor odgovarajućeg metoda veštačke inteligencije pri njihovoj obradi. BREATHE će se baviti ispitivanjem varijabilnosti emisije svetlosti za izabrane bioaerosole različite starosti i vlažnosti koji odgovaraju stanju u atmosferi. Proučavaće se primena novih algoritama za obradu slike radi rekonstrukcije informacije o morfologiji čestica, iz signala rasejanja svetlosti. U projektu će se koristiti metode veštačke inteligencije i nauke o podacima kako bi se napravio klasifikacioni model mašinskog učenja za prepoznavanje i brojanje česticama u realnom vremenu.Takođe, pomoću metoda za objašnjenje rada modela dobiće se inofrmacija o najvažnijim obeležjima koje model koristi pri analizi. Ovo će omogućiti uključivanje domenskog znanja u model koji je prevazhodno zasnovan na podacima i bolju klasifikaciju čestica. Očekuje se da će primena koncepta prenošenja naučenog poboljšati opštost klasifikacionog modela i samim tim njegovu upotrebu na drugim mernim uređajima. Rezultati istraživanja imaju veliki potencijal da dovedu Srbiju na vodeću poziciju u oblasti aerobiologije i atmosferske dijagnostike.
&nbsp;
Sprovođenje ovog projekta je primer kako moderna grupa za atmosfersku dijagnostiku, koja okuplja istraživače iz oblasti aerobiologije, fizike, hemije i nauke o podacima, treba da bude organizovana.
&nbsp;
&nbsp;
<img decoding="async" loading="lazy" class="alignnone size-medium wp-image-1390" src="https://api.biosens.rs/wp-content/uploads/2021/06/Fond-za-nauku-logo-za-oba-projekta-300x101.png" alt="" width="300" height="101" srcset="https://api.biosens.rs/wp-content/uploads/2021/06/Fond-za-nauku-logo-za-oba-projekta-300x101.png 300w, https://api.biosens.rs/wp-content/uploads/2021/06/Fond-za-nauku-logo-za-oba-projekta.png 512w" sizes="(max-width: 300px) 100vw, 300px" />

Naučni savetnik

Dr Sanja Brdar je naučni saradnik i rukovodilac Centra za informacione tehnologije na Institutu BioSens. Doktorirala je na Univerzitetu u Novom Sadu 2016. Pre početka doktorata provela je dve godine u softverskoj kompaniji u timu za razvoj baza podataka. Desetomesečnu Basileus stipendiju za istražvački boravak u Laboratoriji za bioinformatiku na Univerzitetu u Ljubljani dobila je 2010. godine i time postavila osnove za doktorat u oblasti fuzije podataka/znanja u bioinformatici. Aktivno je uključena u mnoge projekte, uključujući H2020 Antares, Dragon, Bestmap i Flekigrobots i predavač je na dva master predmeta na Prirodno-matematičkom fakultetu, smer Nauka o podacima. Njena istraživačka interesovanja uključuju mašinsko učenje, objašnjivu veštačku inteligenciju i bioinformatiku. Radi na ansambalskim metodama, fuziji podataka, klasterizaciji i prediktivnom modelovanju sa primenom u biologiji, poljoprivredi, životnoj sredini i javnom zdravlju. Učesnica je na svetskim izazovima iz nauke o podacima i sa timom istraživača postigla je značajne rezultate: treće mesto na Nokia Mobile Data Challenge (2012), finalista Orange France, Data for Development Challenge (2013), finalista / pobednik / treće mesto na Singenta Crop Challenge (2016, 2017, 2019) i finalista UNDP izazova depopulacije Srbije (2020).

&nbsp;

Dr Marko Panić je naučni saradnik u oblasti tehnološko-tehničkih nauka – informacionih tehnologija na institutu BioSens. Tema doktorata mu je vezana za razvoj algoritama za ubrzanu rekonstrukciju slika iz nepotunih merenja korišćenjem retke reprezentacije signala I statističkih Markovljevih slučajnih modela Njegov pravac istraživanja obuhvata statističko modelovanje multidimenzionalnih podataka dobijenih sa različitih senzora. Trenutno radi na analizi I obradi slika dobijenih sa hiperspektralnih I multispektralnih kamera korišćenjenem naprednih metoda mašinskog učenja sa primenom u proceni kvaliteta voća I povrća. Kao član tima BioSens ucestvovao je na Sindžentinom takmičenju “Izazovu za useve” koje rezltiralo osvajanjem prvog mesta. Aktivno je uključen u mnoge projekte iz poziva Horizont 2020, među kojima su Antares, Cybele, Dragon i Flexirobots, kao i u projekte sa kompanijama poput Krivaje, MK Agri i Delta Agrar.

Gordan Mimić je naučni saradnik na Biosens Institutu. Gordan Mimić je završio osnovne (2011), master (2012) i doktorske (2016) studije fizike-meteorologije na Prirodno-matematičkom fakultetu, Univerziteta u Novom Sadu. Radio je u Republičkom hidrometeorološkom zavodu Srbije tokom perioda 2011-2012, u odeljenju za numeričku prognozu vremena. Gordan Mimić je radio kao asistent na raznim predmetima iz oblasti meteorologije na Univerzitetu u Novom Sadu (Prirodno-matematički fakultet i Poljoprivredni fakultet) u periodu 2012-2017 godina. Trenutno se bavi analitikom podataka u oblasti agrometeorologije i biometeorologije. Predvodio je tim BioSensa koji je razvio novi algoritam za klasifikaciju hibrida kukuruza koji si otporni na sušu i toplotni stress, i za koji su osvojili treću nagradu na Sindžentinom “Izazovu za useve” 2019. godine. Učestvovao je na nekoliko nacionalnih i međunarodnih projekata. Gordan Mimić je koautor 20 naučnih radova, 4 konferencijska rada i 1 poglavlja u knjizi.

Dr Branko Šikoparijaje naučni savetnik u Centru za biosisteme i rukovodilac kvaliteta (ISO17025) u Laboratoriji za palinologiju na Prirodno-matematičkom fakultetu Univerziteta u Novom Sadu. Fokus istraživanja je aerobiolgija, a trenutno je zainteresovan za razvoj detekcije i identifikacije bioaerosola u realnom vremenu. Branko Šikoparija je publikovao i recenzirao naučne radove u brojnim naučnim časopisima. Radi i kao pomoćnik urednika časopisa Aerobiologia. Koordinator je RealForAll mreže za autmatski monitoring bioaerosola u Panonskoj niziji. Takođe, aktivan je član EUMETNET AutoPollen programa, zamenik predsedavajućeg COST Action CA18226, i predsedavajući radne grupe Evropskog Aerobiološkog Udruženja za kontrolu kvaliteta. Vodeći je istraživač BREATHE projekta koji u okviru PROMIS programa finansira Fond za nauku Republike Srbije.

Nacionalni

<img class="alignnone wp-image-1230 size-large" src="https://api.biosens.rs/wp-content/uploads/2021/06/campaigns-1024x401.jpg" alt="" width="1024" height="401" />

&nbsp;
Proučavamo raznovrsnost bioaerosola i procese koji su uključeni u emisiju i disperziju čestica biološkog porekla u atmosferi. Razvijamo sinergiju između merenja bioaerosola u vazduhu i modeliranja njihovog atmosferskog ponašanja. Fokusirajući se na polen i spore gljiva postavili smo temelje za modeliranje aerobioloških pojava i predviđanje njihovog uticaja. Naša istraživanja vode ka razvoju atmosferske dijagnostike a s ciljem pružanja informacija o riziku za zdravlje kako ljudi tako i biljaka i životinja.
&nbsp;
Grupa je počela proučavati polen 1989. godine s naglaskom na prehrambene navike insekata, pogotovo pčela i muva lebdelica. Ovom ekspertizom u saradnji sa društvom pčelara “Dr Jovan Živanovič”, omogućili smo registraciju imena porekla za „Fruškogorski lipov med“. Od 1999. godine istraživanje je usmereno na uzročnike alergija, kada je grupa započela kontinuirano uzorkovanje bioaerosola primenom Hirstovih volumetrijskih klopki za polen i spore.
&nbsp;
U Institutu BioSens, imamo priliku da iskoristimo napredne IT alate kako za uzorkovanje i otkrivanje bioaerosola, tako i za analizu podataka. Nastojimo postaviti temelje za modeliranje atmosferskih koncentracija polena. Stoga povezujemo aerobiološke i satelitske podatke kako bismo mapirali izvore najvažnijeg alergenog polena. Postavljamo terenske eksperimente kako bismo parametrirali emisiju polena.
&nbsp;
Naša grupa takođe istražuje mogućnosti korišćenja protočne citometrije za automstsku detekciju i kvantifikaciju bioaerosola. Trenutno, razvijamo sistem automatskog prećenja polena suspendovanog u vazduhu i poredimo njegove performanse sa klasičnom Hirstovom volumetrijskom metodom i svetlosnom mikroskopijom.
&nbsp;
Posedujemo višegodišnju zbirku uzoraka vazduha iz tipične poljoprivredne oblasti koja je osnov za proučavanje raznovrsnosti bioaerosola i sintetisanje znanja o procesima povezanim sa kretanjem čestica biološkog porekla u atmosferi iznad tipičnih poljoprivrednih i urbanih područja. Takođe imamo referentne signale rasipanja, spektra fluorescence i vremena trajanja fluorescence.
&nbsp;

Projekti:

&nbsp;

2017-2020 “Real-time measurements and forecasting for successful prevention and management of seasonal allergies in Croatia-Serbia cross-border region” –<a href="http://www.realforall.com"> RealForAll</a>, INTERREG IPA-CBC Croatia Serbia

&nbsp;

2020-2022 “Real-time detection and quantification of bioaerosols relevant for human and plant health” –<a href="https://www.realforall.com/language/en/project-breathe/"> BREATHE</a>, Fond za nauku Republike Srbije

&nbsp;

2016-2020 Monitoring polena u vazduhu na teritoriji AP Vojvodine, Pokrajinski sekretarijat za zaštitu životne sredine

BREATHE – Detekcija i kvantifikacija bioaerosola značajnih za zdravlje ljudi i biljaka u realnom vremenu

Teme:

Ljudi:

Centri:

CBS

CIT