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All Journal International Journal of Electrical and Computer Engineering IAES International Journal of Artificial Intelligence (IJ-AI) Jurnal Teknologi Dan Industri Pangan Jurnal Pustakawan Indonesia ComEngApp : Computer Engineering and Applications Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences TELKOMNIKA (Telecommunication Computing Electronics and Control) Jurnal Ilmu Komputer dan Agri-Informatika Jurnal Ilmiah Kursor Biogenesis: Jurnal Ilmiah Biologi Jurnal Teknologi Informasi dan Ilmu Komputer Journal of ICT Research and Applications International Journal of Advances in Intelligent Informatics Indonesian Journal of Biotechnology Seminar Nasional Informatika (SEMNASIF) Sosio Konsepsia Khazanah Informatika: Jurnal Ilmu Komputer dan Informatika Jurnal Teknologi dan Sistem Komputer Jurnal RESTI (Rekayasa Sistem dan Teknologi Informasi) INTENSIF: Jurnal Ilmiah Penelitian dan Penerapan Teknologi Sistem Informasi Jurnal Penelitian Pendidikan IPA (JPPIPA) Kinetik: Game Technology, Information System, Computer Network, Computing, Electronics, and Control ILKOM Jurnal Ilmiah Jurnal Nasional Pendidikan Teknik Informatika (JANAPATI) Komputasi: Jurnal Ilmiah Ilmu Komputer dan Matematika Jurnal Jamu Indonesia Journal of Electronics, Electromedical Engineering, and Medical Informatics VISI PUSTAKA: Buletin Jaringan Informasi Antar Perpustakaan JURNAL Al-AZHAR INDONESIA SERI SAINS DAN TEKNOLOGI Indonesian Journal of Electrical Engineering and Computer Science Nusantara Science and Technology Proceedings Bioinformatics and Biomedical Research Journal Jurnal Pustakawan Indonesia Jurnal Nasional Teknik Elektro dan Teknologi Informasi J-Icon : Jurnal Komputer dan Informatika Indonesian Journal of Jamu
Wisnu Ananta Kusuma
Department Of Computer Science, Faculty Of Mathematics And Natural Sciences, IPB University, Jl Meranti Kampus IPB Dramaga, Bogor 16680, Indonesia
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Chemical Engineering, Chemistry & Bioengineering Chemistry Computer Science & IT Control & Systems Engineering Decision Sciences, Operations Research & Management Economics, Econometrics & Finance Education Electrical & Electronics Engineering Energy Engineering Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Law, Crime, Criminology & Criminal Justice Library & Information Science Materials Science & Nanotechnology Medicine & Pharmacology Physics Public Health Social Sciences Other

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Algorithm for Predicting Compound Protein Interaction Using Tanimoto Similarity and Klekota-roth Fingerprint Isnan Mulia; Wisnu Ananta Kusuma; Farit Mochamad Afendi
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 16, No 4: August 2018
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v16i4.5916

Abstract

This research aimed to develop a method for predicting interaction between chemical compounds contained in herbs and proteins related to particular disease. The algorithm of this method is based on binary local models algorithm, with protein similarity section is omitted. Klekota-Roth fingerprint is used for the compound's representation. In the development process of the method, three similarity functions are compared: Tanimoto, Cosine, and Dice. Youden’s index is used to evaluate optimum threshold value. The result showed that Tanimoto similarity function yielded higher similarity values and higher AUC value than those of the other two functions. Moreover, the optimum threshold value obtained is 0.65. Therefore, Tanimoto similarity function and threshold value 0.65 are selected to be used on the prediction method. The average evaluation accuracy of the developed algorithm is only about 50%. The low accuracy value is allegedly caused by the only use of compound similarity on the prediction method, without including the protein similarity.
Fuzzy-based Spectral Alignment for Correcting DNA Sequence from Next Generation Sequencer Kana Saputra S; Wisnu Ananta Kusuma; Agus Buono
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 14, No 2: June 2016
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v14i2.2395

Abstract

Next generation sequencing technology is able to generate short read in large numbers and in a relatively short in single running programs. Graph based DNA sequence assembly used to handle these big data in assembly step. The graph based DNA sequence assembly is very sensitive to DNA sequencing error. This problem could be solved by performing an error correction step before the assembly process. This research proposed fuzzy inference system (FIS) model based spectral alignment method which can detect and correct DNA sequencing error. The spectral alignment technique was implemented as a pre-processing step before the DNA sequence assembly process. The evaluation was conducted using Velvet assembler. The number of nodes yielded by the Velvet assembler become a measure of the success of error correction. The results shows that FIS model based spectral alignment created small number of nodes and therefore it successfully corrected the DNA reads.
Identification of Tuna and Mackerel based on DNA Barcodes using Support Vector Machine Mulyati Mulyati; Wisnu Ananta Kusuma; Mala Nurilmala
TELKOMNIKA (Telecommunication Computing Electronics and Control) Vol 14, No 2: June 2016
Publisher : Universitas Ahmad Dahlan

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.12928/telkomnika.v14i2.2469

Abstract

Tuna and mackerel are important fish in Indonesia that have great demand in the community and contain good nutrients for health. Many of the processed products have been faked including processed fish, by replacing the content of products that have high sales value to other lower price one. For ensuring food safety, fraudulent should be prevented by identifying the content of refined product. In this research, we implemented support vector machine (SVM), one of the popular methods in machine learning, to yield a model for identifying the content of refined product based on DNA barcode sequences. The feature extraction of DNA barcode Sequences was conducted by calculating k-mers frequency of each sequences. In this study, we used trinucleotide (3-mers) and tetranucleotide (4-mers). These features were inputted to SVM to classify and identify whether the DNA barcode sequences belong to the class of tuna, mackerel, or other fish. The evaluation results showed model SVM was able to perform identification with the accuracy 88%.
BEBERAPA PENCIRI BERBASIS SEKUENS UNTUK MENGENALI SIFAT FUNGSIONAL PEPTIDA BIOAKTIF: STUDI EKSPLORASI Badrut Tamam; Dahrul Syah; Hanifah Nuryani Lioe; Maggy T. Suhartono; Wisnu Ananta Kusuma
Jurnal Teknologi dan Industri Pangan Vol. 29 No. 1 (2018): Jurnal Teknologi dan Industri Pangan
Publisher : Departemen Ilmu dan Teknologi Pangan, IPB Indonesia bekerjasama dengan PATPI

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (280.199 KB) | DOI: 10.6066/jtip.2018.29.1.1

Abstract

Bioactive peptides have important role as functional food ingredients. The sequence patterns of amino acids in peptide fragments may relate to their functional mechanisms. On the contrary, presence of an amino acid in a peptide fragment might not be sufficient to provide a unique identifier toward the bio-active peptide functional properties as antihypertensive (AH), antioxidative (AO) or antimicrobial (AM) agents. The main objective of this study was to explore the identifiers of bioactive peptides based on the sequence-generated properties. This study was performed using meta-analysis by utilizing many data sources and qualified international journal publications. The identifiers of bioactive peptides include sequence length, molecular weight, isoelectric point (pI), net charge and hydrophobicity. Based on the average score of the five identifiers, antimicrobial (AM) peptides were very different from antihypertensive (AH) and antioxidative (AO) peptides. The comparisons of the peptide biofunctional properties based on the identifiers may be determined as follows: AH1<AO1<AM1 (for sequence length); AH1<AO1<AM1 (for molecular weight); AH1=AO1<AM1 (for isoelectric point/pI); AH1=AO1<AM1 (for net charge) and AH1<AM1<AO1 (for hydrophobicity).
Performance Comparison of Data Sampling Techniques to Handle Imbalanced Class on Prediction of Compound-Protein Interaction Akhmad Rezki Purnajaya; Wisnu Ananta Kusuma; Medria Kusuma Dewi Hardhienata
Biogenesis: Jurnal Ilmiah Biologi Vol 8 No 1 (2020)
Publisher : Department of Biology, Faculty of Sci and Tech, Universitas Islam Negeri Alauddin Makassar

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.24252/bio.v8i1.12002

Abstract

The prediction of Compound-Protein Interactions (CPI) is an essential step in the drug-target analysis for developing new drugs as well as for drug repositioning. One challenging issue in this field is that commonly there are more numbers of non-interacting compound-protein pairs than interacting pairs. This problem causes bias, which may degrade the prediction of CPI. Besides, currently, there is not much research on CPI prediction that compares data sampling techniques to handle the class imbalance problem. To address this issue, we compare four data sampling techniques, namely Random Under-sampling (RUS), Combination of Over-Under-sampling (COUS), Synthetic Minority Over-sampling Technique (SMOTE), and Tomek Link (T-Link). The benchmark CPI data: Nuclear Receptor and G-Protein Coupled Receptor (GPCR) are used to test these techniques. Area Under Curve (AUC) applied to evaluate the CPI prediction performance of each technique. Results show that the AUC values for RUS, COUS, SMOTE, and T-Link are 0.75, 0.77, 0.85 and 0.79 respectively on Nuclear Receptor data and 0.70, 0.85, 0.91 and 0.72 respectively on GPCR data. These results indicate that SMOTE has the highest AUC values. Furthermore, we found that the SMOTE technique is more capable of handling class imbalance problems on CPI prediction compared to the remaining three other techniques.
Analysis using top‐k skyline query of protein‐protein interaction reveals alpha‐synuclein as the most important protein in Parkinson’s disease Mohammad Romano Diansyah; Annisa Annisa; Wisnu Ananta Kusuma
Indonesian Journal of Biotechnology Vol 26, No 4 (2021)
Publisher : Universitas Gadjah Mada

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.22146/ijbiotech.63023

Abstract

Parkinson’s disease is the second‐most‐common neurodegenerative disorder and can reduce patients’ quality of life. The disease is caused by abnormalities in dopaminergic neurons, such as reactive oxygen species (ROS) imbalance leading to programmed cell death, protein misfolding, and vesicle trafficking. Protein‐protein interaction (PPI) analysis has been demonstrated to understand better candidate proteins that might contribute to multifactorial neurodegenerative diseases, particularly in Parkinson’s disease. PPI analysis can be obtained from experiments and computational predictions. However, experiment data is often limited in interactome coverage. Therefore, additional computational prediction methods are required to provide more comprehensive PPI information. PPI can be represented as protein‐protein networks and analyzed based on centrality measures. The previous study has shown that top‐k skyline query, a method using dominance rule‐based centrality measures, reveals important protein candidates in Parkinson’s diseases. This study applied the top‐k skyline query to PPIs containing experiment and prediction data to find important proteins in Parkinson’s disease. The result shows that alpha‐synuclein (SNCA) is the most important protein and is expected to be a potential biomarker candidate for Parkinson’s disease.
PENGEMBANGAN VISUAL INTERACTIVE SIMULATION DALAM SISTEM PENUNJANG KEPUTUSAN DENGAN PENDEKATAN AGEN (Studi Kasus Investasi pada Industri Biodisel Kelapa Sawit) Prihasuti Harsani; Sri Nurdiati; Wisnu \ Ananta Kusuma
Seminar Nasional Informatika (SEMNASIF) Vol 1, No 3 (2008): Intelligent System dan Application
Publisher : Jurusan Teknik Informatika

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Abstract

Sistem Penunjang Keputusan dengan simulasi dapat menjadi efektif dengan pemanfaatan Visual Interactive Simulation (VIS). Melalui VIS pengambil keputusan mengontrol sepenuhnya jalannya simulasi dengan penentuan skenario dan modifikasi parameter simulasinya.  Pembangunan sistem dengan VIS dilakukan dengan metodologi gaia untuk memodelkan sistem agen. Melalui gaia, dihasilkan lima model utama sebagai dasar pembentukan arsitektur sistem, yaitu model interaksi, model role, model service, model acquitance dan model agen. Pendefinisian arsitktur sistem yang lebih konkret dilakukan melalui Agent Unified Modelling Languagae (AUML)
AUTONOMOUS MOBILE ROBOT MENGGUNAKAN METODE FORMAL LOGIKA TEMPORAL LINIER Irvan Lewenusa; Wisnu Ananta Kusuma
Seminar Nasional Informatika (SEMNASIF) Vol 1, No 2 (2008): Instrumentational And Robotic
Publisher : Jurusan Teknik Informatika

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Abstract

Logika temporal linier (LTL) dikontruksi dari formulasi logika tingkah laku sistem yang diharapkan dari waktu ke waktu secara linier. Dengan demikian jika pada bagian atau waktu tertentu terjadi kesalahan pada sistem, kesalahan itu dapat segera diantisipasi. Dalam hal ini penggunaan perencanaan logika temporal linier tidak hanya digunakan pada autonomous mobile robot untuk mencapai sebuah tujuan atau menghindari rintangan, tetapi juga untuk perangkaian, perluasan atau penugasan sementara (temporal ordering) pada sebuah rangkaian tugas yang berbeda dalam satu waktu. Dalam LTL untuk menghasilkan lintasan robot dilakukan tiga tahap tahap aktivitas, yaitu pendefinisan abstraksi diskrit pergerakan robot, perencanaan logika temporal menggunakan model checking, dan implementasi kontinu rencana diskret (continuous implementations of discrete plan).Pada penelitian ini, untuk membuktikan apakah model perencanaan logika temporal linier yang dibuat sebelumnya memenuhi spesifikasi tingkah laku sebuah mobile robot yang dimaksud, maka dibuatlah sebuah autonomous mobile robot sebagai alat uji implementasi formula logika temporal linier tersebut.  Untuk membangun sebuah autonomous mobile robot tersebut diperlukan beberapa perangkat elektronika di antaranya mikrokontroler, sensor, kompas, dan motor penggerak. Selain itu dilakukan pula simulasi dengan perangkat lunak MOBOTSIM versi 1.0.03.Implementasi formulasi dengan simulasi menggunakan  MOBOTSIM menunjukkan hasil yang lebih ideal daripada pembangunan formulasi pada robot sebenarnya Hal ini disebabkan pergerakan protipe mobile robot banyak dipengaruhi faktor luar  yang dalam penelitian ini diabaikan.
PENGEMBANGAN ENTERPRISE RESOURCE PLANNING (ERP) UNTUK PERUSAHAAN RITEL Halida Ernita; Wisnu Ananta Kusuma
Seminar Nasional Informatika (SEMNASIF) Vol 1, No 5 (2008): Information System And Application
Publisher : Jurusan Teknik Informatika

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Abstract

Ritel memiliki peranan penting dalam proses pendistribusian produk dan jasa dari produsen ke konsumen. Ritel membutuhkan pengaturan informasi bagi konsumen dan produsen mengenai produk dan jasa yang tersedia dan yang diperlukan. Perubahan yang cepat pada lingkungan ritel saat ini, menuntut pengusaha untuk lebih cerdas dan tanggap terhadap perubahan tersebut. Enterprise Resource Planning (ERP) merupakan sebuah sistem yang dapat mengatasi permasalahan tersebut. ERP merupakan sebuah sistem yang mengintegrasikan proses bisnis perusahaan sehingga dapat merampingkan aktivitas perusahaan, memfasilitasi interaksi antar unit bisnis, dan memberikan kemudahan untuk mengakses informasi. Dipicu oleh perkembangan e-commerce saat ini, fungsi pada ERP juga mengalami penambahan  yaitu adanya interaksi bisnis secara elektronik. Pada Penelitian ini dikembangkan sebuah sistem Enterprise Resource Planning untuk perusahaan ritel dimana fungsi-fungsi dalam sistem ini disesuaikan dengan  kebutuhan e-commerce. ERP ini akan dibangun dengan pendekatan berorientasi objek dan memanfaatkan design pattern  Model View Controller (MVC)  pattern.
Perancangan Next Generation OPAC Berbasis Library 2.0 (Next Generation OPAC Design Based on Library 2.0) Toni Afandi; Wisnu Ananta Kusuma; Janti G. Sudjana
Jurnal Pustakawan Indonesia Vol. 13 No. 1 (2014): Jurnal Pustakawan Indonesia
Publisher : Perpustakaan IPB

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (480.247 KB) | DOI: 10.29244/jpi.13.1.%p

Abstract

ABSTRACTLibrary catalogue is challenged by the development of web technology that produce search engines dan also has change users’ interaction with information in this Web 2.0 enviroment. Users expect to participate and collaborate in the creation of information. This study aims to create a prototype of next generation OPAC which will use users’ contribution as an enrichment to OPAC. Users can contribute information to existing bibliographic record with tagging, rating and comment. Prototype was created using Drupal 7 and tested using Black Box method. Testing results shows that this prototype can fufill all functional requirements.Keywords: next generation OPAC, Web 2.0, Library 2.0, tagging, rating, review.
Co-Authors Abdul Aziz Abdul Rahman Saleh Adrianus, Albert Afifa, Rizky Maulidya Agus Buono Ahmad, Tarmizi Aini Fazriani Aisah Rini Susanti Alami, Tegar Ali Djamhuri Annisa Annisa Annisa , Annisa Annisa Annisa Annisa Annisa Annisa Annisa Annisa Annisa Anton Suryatama Arini Aha Pekuwali Arini Pekuwali Arwan Subakti Ary Prabowo Ary Prabowo Auliatifani, Reza Auliya Ilmiawati Auriza Rahmad Akbar Azizah, Norma Nur Azzahra, Syarifah Fathimah Badollahi Mustafa Badrut Tamam Bahrul Ulum Budi Tjahjono Dahrul Syah Diah Handayani Dian Indah Savitri Dian Kartika Utami Essy Harnelly Fadli , Aulia Fahrury Romdendine, Muhammad Farhan Ramadhani , Hilmi Farit Mochamad Afendi Farohaji Kurniawan Fatriani, Rizka Fazriani, Aini Firman Ardiansyah Ginoga, Muh Fadhil Al-Haaq Halida Ernita Handayani, Vitri Aprilla Handayani, Vitri Aprilla Hanifah Nuryani Lioe Hardi, Wishnu Hasibuan, Lailan Sahrina Hendra Rahmawan Hendra Rahmawan Hera Dwi Novita Heru Sukoco Imas Sukaesih Sitanggang Indra Astuti Ira Maryati Irfan Wahyudin Irma Herawati Suparto Irman Hermadi Irmanida Batubara Irvan Lewenusa ISKANDAR ZULKARNAEN SIREGAR Isnan Mulia Janti G. Sudjana Jaya Sena Turana Joni Prasetyo Kana Saputra S Kangko, Danang Dwijo Karlisa Priandana Khaydanur Khaydanur Khaydanur, Khaydanur Laela Wulansari Larasati Larasati Lina Herlina Tresnawati Listina Setyarini Lusi Agus Setiani M. Rafi Maggy T. Suhartono Mala Nurilmala Medria Kusuma Dewi Hardhienata Mohamad Rafi Mohamad Rafi Mohamad Rafi Mohammad Romano Diansyah Mohammad Romano Diansyah Muchlishah Rosyadah Muhammad Asyhar Agmalaro Muhammad Subianto Mulyati Mulyati Mushthofa Muttaqin, Muhammad Rafi Nasution, Tegar Alami Nengsih, Nunuk Kurniati Norma Nur Azizah Nunuk Kurniati Nengsih Nur Choiriyati Nurdevi Noviana Ovi Sofia Pramita Andarwati Prihasuti Harsani Priyo Raharjo Pudji Muljono Purnajaya, Akhmad Rezki Purnomo, Tsania Firqin Ramadhanti, Nabila Sekar Ramdan Satra Ratu Mutiara Siregar Refianto Damai Darmawan Refianto Damai Darmawan Resnawati Reza Auliatifani Rif’ati, Lutfah Ronald Marseno Rosy Aldina Rosyadah, Muchlishah Rudi Heryanto SATRIYAS ILYAS Septaningsih, Dewi Anggraini Siti Syahidatul Helma Sony Hartono Wijaya Sri Nurdiati SUHARINI, YUSTINA SRI Sulistyo Basuki Sulistyo Basuki Supriyanto, Arif Syahid Abdullah Syarifah Aini Syukriyansyah Taufik Djatna Toni Afandi Tsania Firqin Purnomo Usman, Muhammad Syafiuddin Wa Ode Rahma Agus Udaya Manarfa Wahjuni, Sri Widya Sari Wijaya, Eko Praja Hamid Wina Yulianti Wishnu Hardi Wulansari, Laela Yandra Arkeman Yessy Yanitasari Yudhi Trisna Atmajaya Yulianah Yulianah Yunita Fauzia Achmad Zulkarnaen, Silvia Alviani