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4th International Conference on Cybernetics and Intelligent System, ICORIS 2022

作者： Azizatikarna, Kians Parung, Deby Erina Amirullah, Dian Hidayat, Alam Ahmad Cenggoro, Tjeng Wawan Budiarto, Arif Simon Pardamean, Bens Genetics Indonesia Jakarta12940 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bina Nusantara University BINUS Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665453950

As the cost of genetic testing becomes more affordable each year, direct-to-customer (DTC) genetic testing services witness rapid market growth. This has encouraged the development of an easy-to-use website application to optimize potential customers to obtain informed choice regarding the offered DTC genetic testing as well as purchasing information. We present a wireframing process as a part of the agile software development process to build a web portal prototype for an Indonesia-based genetic testing service called DNAku. The approach in building the prototype used in this case is a part of the Agile Software Development Method. In brief, the wireframing stage resulted in this work consists of three main important outcomes. The first one is the use case diagram as a blueprint of this web-based system. A site map is then proposed as an extended version of the use case diagram which visualizes the whole pages with the links. Finally, based on this site map a series of page mock-ups are designed using Hyper Text Marking Language (HTML) and Cascading Style Sheets (CSS). The result of the prototype can be used as the basis for the next development stage, which is the coding stage based on the collected feedback from users. Considering the continuous application development via the wireframing method by taking into account the cycle of feedbacks from involved parties, this approach can strengthen the infrastructure to sustain DTC genetic business model, which has a niche market in Indonesia. © 2022 IEEE.

关键词： Sales

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miR-let-7a-2, miR103a-2 and CREB1-TF as therapeutic targets to regulate the transcription of DISC1 and PDE4D in the transcriptional regulation pathway by DISC1/ATF4 complex

miR-let-7a-2, miR103a-2 and CREB1-TF as therapeutic targets ...

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BioInspired Processing (BIP), IEEE International Conference on

作者： Esteban José Rodríguez Rodríguez Rodrigo Mora-Rodríguez Celular and Molecular Research Center (CIBCM) University of Costa Rica San José Costa Rica Master Program of Bioinformatics and System Biology Posgraduate Program SEP University of Costa Rica San José Costa Rica

ISBN: (纸本)9781665470490

Disrupted In Schizophrenia 1 (DISC1) is considered a multifunctional protein implicated in various signaling pathways with neurological relevant outcomes, with the Disrupted In Schizophrenia 1/Activating Transcription Factor 4 (DISC1/ATF4) transcriptional regulation pathway being a pathway of interest since it regulates Phosphodiesterase 4D (PDE4D) transcription. Alterations in the transcription levels of DISC1 and PDE4D have been implicated in neurodegenerative processes and the identification of therapeutic targets that regulate these processes can be of great help to promote neuroprotective processes. By using a System Biology approach, we created a mathematical model of the transcriptional regulation of the DISC1/ATF4 pathway and using this model we conducted in-silico experiments to identify potential therapeutic targets with robust control on the network. As a result, miR-let-7a-2 is reported as a transcriptional regulator of DISC1 as well as miR103-a2 and CREB1-TF as transcriptional regulators of the PDE4D. These three regulators are identified as in-silico therapeutic targets to promote neuroprotective processes against neurodegenerative mental disorders.

关键词： Robust control Proteins Regulators Mental disorders Biological system modeling Systems biology Regulation

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Development of technology and engineering: Cases of study of the bioinformatics and biology sistems master's Degree in Costa Rica

Development of technology and engineering: Cases of study of...

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IEEE Central America and Panama Convention (CONCAPAN)

作者： Vanesa Mora Hernández Federico Matarrita José Molina Mora Luis Rojas Matey Eduardo Quiros Man Sai Edwin Báez Luis Ruiz Ricardo Boza Allan Orozco Biomedical Sciences Program and Bioinformatics Master's degree School of Medicine University of Costa Rica (UCR) San Jose Costa Rica Autonomous University of Madrid (UAM) Spain

ISBN: (纸本)9781467395793

This work is based on the bioinformatics technology developments made on the post graduate course of the bioinformatics master's Degree of the University of Costa Rica's Medical School, imparted by Professor Allan Orozco, who is one of the main academic founders of master's Degree. The biocomputing programs were developed by several students that cover the innovation and development of sequence alignment programs by using bar codes with color spectrum differentiation. Its includes a web, noise elimination techniques on microarrays, solution algorithms of Smith-Waterman in Delphi language, it's also provides a way to design and implementation of a new system to build workflows (WORFORBIO: Workflows for bioinformatics) and a text mining system on the Protein Data Bank based on SOLR APACHE and REST. Web services from Medical School's GALAXY server at the NELLY bioinformatics Cluster were used to make complimentary tests.

关键词： bioinformatics Tools Proteins Algorithm design and analysis Data models Text mining Libraries

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Data annotation system for intelligent energy conservator in smart building 3

Data annotation system for intelligent energy conservator in...

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3rd International Conference on Eco Engineering Development, ICEED 2019

作者： Pardamean, Bens Cenggoro, Tjeng Wawan Chandra, Bloomest Jansen Rahutomo, Reza Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department College of Letters and Science University of Wisconsin MadisonWI53706 United States Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia

The concept of smart building includes the optimization of energy usage in a building. One of the possible solutions for this is to adaptively adjust appliances utilization according to activity level in the building. Thus, an intelligent activity estimation system needs to be developed. However, massive annotated dataset is necessary to train the system. Therefore, we propose a system that enables rapid data annotation to collect the massive dataset. With the proposed system, an image can be annotated within 4.8 seconds in average. © 2020 Published under licence by IOP Publishing Ltd.

关键词： Historic preservation

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Multivariate Time-Series Deep Learning for Joint Prediction of Temperature and Relative Humidity in a Closed Space 8

Multivariate Time-Series Deep Learning for Joint Prediction ...

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8th International Conference on Computer Science and Computational Intelligence, ICCSCI 2023

作者： Gunawan, Fergianto E. Budiman, Arief S. Pardamean, Bens Juana, Endang Romeli, Sugiarto Cenggoro, Tjeng W. Purwandari, Kartika Hidayat, Alam A. Redi, Anak A.N.P. Asrol, Muhammad Industrial Engineering Department BINUS Graduate Program - Master of Industrial Engineering Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Electrical Engineering Department Faculty of Industrial Technology Universitas Trisakti Jakarta11440 Indonesia PT Impack Pratama Industri Jakarta14350 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Mathematics Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia

An accurate predictive model of temperature and humidity plays a vital role in many industrial processes that utilize a closed space such as in agriculture and building management. With the exceptional performance of deep learning on time-series data, developing a predictive temperature and humidity model with deep learning is propitious. In this study, we demonstrated that deep learning models with multivariate time-series data produce remarkable performance for temperature and relative humidity prediction in a closed space. In detail, all deep learning models that we developed in this study achieve almost perfect performance with an R value over 0.99. © 2023 The Authors. Published by Elsevier B.V.

关键词： closed space deep learning humity prediction indoor temperature prediction

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The effect of visual advanced driver assistance systems on a following human driver in a mixed-traffic condition

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Procedia Computer Science 2023年 216卷 221-229页

作者： Dedy Ariansyah Bens Pardamean Giandomenico Caruso Bioinformatics and Data Science Research Centre Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program Master of Computer Science Program Bina Nusantara University Jakarta 11480 Indonesia Department of Mechanical Engineering Politecnico di Milano Milan 20156 Italy

Rapid development in vehicular technology has caused more automated vehicle control to increase on the roads. Studies showed that driving in mixed traffic with an autonomous vehicle (AV) had a negative impact on the time headway (THW) of conventional vehicles (CVs) (i.e., driven by humans). To address this issue, there is a need to equip CV with visual advanced driver assistance systems (ADASs) that helps the driver maintain safe headway when driving near AVs. This study examines the perception of drivers using visual ADAS and their associated risk while driving behind the AV at constant and varying speeds. The preliminary results showed that while visual ADAS could help drivers keep the safe THW, it could affect drivers’ ability to react to emergencies. This implies that visual modality alone might not be sufficient and therefore requires some other feedback or intelligent transport systems to help drivers maintain safe driving in a mixed-traffic condition.

关键词： sustainable transport management platooning car-following visual advanced driver assistance system virtual realtiy

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miRNA networks regulating gene expression in response to tension or compression forces in the cells of the periodontal ligament

miRNA networks regulating gene expression in response to ten...

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BioInspired Processing (BIP), IEEE International Conference on

作者： Mariana Bonilla Valverde Rodrigo Mora Rodríguez Master Program on Bioinformatics and Systems Biology Postgraduate Program SEP University of Costa Rica 11501-2060 San José Costa Rica Faculty of Microbiology University of Costa Rica 11501-2060 San José Costa Rica

ISBN: (纸本)9781665470490

In response to force application, biological reactions occur in the periodontal ligament that causes the orthodontic tooth movement. Differential expression of genes such as ALPL, FGF7, PDRM1, and NR4A2 are involved in the exposure to tension or compression forces by contributing to bone remodeling. In this study, a systems biology approach is used in order to identify a modulator of gene expression when mechanical loadings are applied in periodontal ligament cells. We developed a mathematical model of the interaction network of ALPL and FGF7 with several miRNAs and the transcription factor modulators in BioNetUCR, Cytoscape and COPASI software. We found that miR129-2 has a negative control in ALPL, FGF7, NR4A2 and PRDM1 genes, while miRNA192 has a negative control in ALPL and FGF7 genes in compression and tension side. Both miRNAs are proposed for future experimental validation.

关键词： Systems biology Loading Force Modulation Cells (biology) Bones Software

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A Systems Biology Approach to Identify Candidate Targets to Downregulate Angiogenic Gene Expression in Cancer

A Systems Biology Approach to Identify Candidate Targets to ...

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International Work Conference on Bio-inspired Intelligence (IWOBI)

作者： Calderon-Gomez Paola Man-Sai Aeón-Chan RA Mora-Rodriguez Master Program on Bioinformatics and Systems Biology University of Costa Rica (UCR) San José Costa Rica Faculty of Microbiology University of Costa Rica (UCR) San José Costa Rica

The control of angiogenesis in cancer has been recognized as a promising therapeutic target for many diseases like cancer. Specifically, the Angiopoietin-2 - Vascular Endothelial Growth Factor system has demonstrated special relevance in the regulation of angiogenesis, highlighting the importance of the complex coordination among vascular signaling molecules [3] for the identification of targets for future anti-angiogenic therapy. Current approaches to regulate the angiogenesis process focus their efforts only on VEGF regulation but this has proven ineffective in many kinds of cancer, prompting the need for further understanding of how the vasculature can be effectively targeted in tumors [9]. Given the complex properties of gene expression in this process, a Systems Biology approach is required to identify putative candidates to robustly regulate genes involved in angiogenesis. We propose a model with candidate targets to downregulate the angiogenic genes expression. We identified a strong regulation of the AKT1-ANGPT2-KDR axis by miR200B and miR200C. Also, we identified a strong regulation of SRC by miR34a. These candidate miRNAs could therefore have a potential for the development of novel therapeutic strategies against angiogenesis in cancer.

关键词： Biological system modeling Cancer Analytical models Data models Tumors Systems biology Mathematical model

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Implementation of Face Patterns and Smile Recognition for Intelligent Class Attendance Systems 6

Implementation of Face Patterns and Smile Recognition for In...

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6th International Conference on Computer and Informatics Engineering, IC2IE 2023

作者： Miftakhurrokhmat Suparyanto, Teddy Elwirehardja, Gregorius Natanael Karimah, Shofiyati Nur Pardamean, Bens Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta Indonesia School of Computer Science Bina Nusantara University Computer Science Department Jakarta Indonesia Universitas Amikom Yogyakarta Faculty of Computer Science Department of Informatics Yogyakarta Indonesia Bina Nusantara University Binus Graduate Program - Master of Computer Science Computer Science Department Jakarta Indonesia

ISBN: (纸本)9798350345162

Students 'attendance in class is one important success parameter in face-to-face learning processes. Conventional attendance systems, such as paper-based attendance sheets or identity card systems, require a long time in the manual recapitulation process. Without additional verifications, even computer vision-based methods are prone to fraudulent practices by the students instead of gaining their excitement and attention in a class. To stimulate students' attention in a class, this work designs an intelligent class attendance system, in which facial pattern and smile recognition are implemented by using the latter as an additional task-based verification to reduce the risks of fake attendance. For the face recognition module, this pilot study used FaceNet as a feature extractor combined with SVM for classification, whereas the Haar cascade algorithm is used for recognizing smiles. This face recognition pipeline was implemented as a service installed on minicomputers or Internet of Things (IoT) devices in each classroom and connected to an IP camera. Every recorded attendance will be sent as a notification to a mobile application for students that requires their active participation to confirm it with a smiling self-photo. The proposed pipeline obtained 92.86% accuracy on the test data, and 66.67% accuracy when evaluated in a real-life simulation setting through the implemented system. The lower accuracy in the simulation indicated that further improvements are indispensable, especially since the model obtained 28.57% False Negative Rate. Future studies will need to acquire more data and experiment with more efficient methods of attendance verification. © 2023 IEEE.

关键词： class attendance convolutional neural network deep learning face recognition smile

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IoT Solution for Intelligent Pond Monitoring 3

IoT Solution for Intelligent Pond Monitoring

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3rd International Conference on Eco Engineering Development, ICEED 2019

作者： Darmalim, Usin Darmalim, Ferdinan Darmalim, Sutristo Hidayat, Alam Ahmad Budiarto, Arif Mahesworo, Bharuno Pardamean, Bens Mega Medica Pharmaceuticals Jakarta11840 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta11480 Indonesia

Channa striata or the striped snakehead fish is one of snakehead fish species which inhabits all types of freshwater bodies distributed across Asian countries. Because this fish is known to have higher albumin fraction (64.61%) of protein and other economic values, domestication, and cultivation of this fish has been done in many Asian countries such as Indonesia, China, Malaysia, Thailand, Bangladesh, and India. Environmental factors such as temperature, water pH, dissolved oxygen, total dissolved solids, and turbidity are important parameters must be considered inbreeding and growing this type of fish. The aim of this paper is to propose an IoT solution to automatically monitor these environmental factors. It is designed with affordable and open-source electrical components to provide a cost-efficient solution for farmers. Five sensors are used to measure each parameter. A web application prototype is also presented as a companion application for the users to get useful information from the IoT device. It is developed using a Pythonframework. By accessing this web application, the users can immediately detect any abnormal conditions of the pond. © 2020 Published under licence by IOP Publishing Ltd.

关键词： Fish

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