- Bioinformatics Research Group (BIRG)
Department of Biological Sciences,
Faculty of Biosciences and Bioengineering
Universiti Teknologi Malaysia
81310 Skudai, Johor
MALAYSIA
- Biology, Biodiversity, Structural Biology, Agrobiodiversity, Computational Biology, Chemical Ecology, and 18 moreMolecular Dynamics Simulation, Education, Bioinformatics, Photography, Cloud Computing, Science Education, Ethnobotany, Plant Biology, Phytochemistry, Environmental Monitoring, Ethnobiology, Fertility, Cluster Computing, Distributed/mobile Computing, Prion Diseases, Bioinformatics Malaysia, Commodity Hardware, and Education Policyedit
- Research Interests Biodiversity informatics, biodiversity databases, visualisation of data and data curation for bio... moreResearch Interests
Biodiversity informatics, biodiversity databases, visualisation of data and data curation for biodiversity. Using Molecular Dynamics in studying protein folding, behaviour and conformations especially those related to conformational diseases. Other interests are in the area of pedagogy used in bioinformatics education.
Current Projects
Johor Biodiversity Database (JBIODI)
In this project we showcase JBiodi, a biodiversity informatics database created to warehouse the biodiversity information on indigenously found species in the state of Johor. The database is aimed to be web based platform to be curated using only a web browser through a novel content management system in real time. Recently, ethonobotanical and phytochemical databases have increased in their prominence as stakeholders in biodiversity began to catalogue and document massive ethnomedical knowledge and digitise legacy biodiversity data. Therefore, we have populated the database with 150 exemplar pages showing ethnomedicinal plants found in Johor. Apart from the typical taxonomical features found in similar biodiversity databases, JBiodi has several additional functionalities. First, active compounds identified from ethnomedicinal plants has a link to PubChem database which allows users to view chemical structure using Jmol applet. Second, links are created to external sites such as distribution pattern in GBIF, literature in Scirus and legacy publication in Biodiversity Heritage library. Future functionalities would include GIS maps of Johor and expanded capabilities to analyse geospatial distribution of species.
Other Biodiversity Database Projects
Portal
http://www.biodiversity.my
http://birg1.fbb.utm.my/jbiodi/index.php
My Faculty
http://www.bioscience.utm.my
Malaysian Frogs, amphibian etc
http://amphibia.my/amphibians.php
Malaysia reptiles
http://amphibia.my/reptiles.php?type=reptiles
Mangroves of Langkawi
http://biodiversity.my/mangrove/
Visualizing of Biodiversity Using GIS (VIBIGIS)
VIBIGIS is web based biodiversity and ecosystem informatics content management system that is designed for the numerous scattered ecological and biodiversity data typically found in Malaysian research community. It is an online biodiversity database system integrated with established GIS applications with a centralized enterprise repository. Interactive visualization provides an effective way of presenting large amounts of complex information to a wide audience, especially those with no experience of GIS or mapping, as it provides the user with visual cues that are more intuitive than those of a conventional map. It is a scalable database that provides variable and adaptable feature modification for its users. It is also designed to incorporate different layers of knowledge to allow selective viewing to protect sensitive indigenous biodiversity data. The use of spatial information will enable researcher to analyze ecological trends and behavior. The database is also accessible via the web for easy data population and curation.
http://birg2.fbb.utm.my/page.php?pageid=biodi_gis
Mersing Biodiversity Map
Biodiversity informatics is a currently developing bioinformatics field that contributes to the management of the biodiversity and ecosystem by providing decision making cues to researchers, environmental managers and policymakers. It brings together ecologist, environmentalist and computer scientists to solve real-world conservation challenges while developing the underlying ecological, bioinformatics, and information sciences. However, biodiversity information is currently presented in textual databases making access difficult or even inaccessible and with existing geospatial information in numbered coordinates that is almost
meaningless in first instance. Therefore, there is a practical need for biodiversity and ecosystem data to be integrated, hence both geo-referenced and "species-referenced" to aid visualisation and explore species distribution conveniently. In this paper, we present a web based Rich-Internet Application (RIA) as an interactive visualization tool to provide an effective way of view large amounts of complex biodiversity information. We have chosen the Johor East Coast as the base map to allow EKOMAR researchers to utilise it as a one stop portal for biodiversity research. It is designed to appeal to a wider audience, especially those with no experience of GIS or mapping, as it provides the user with visual cues that are more intuitive than those of a conventional digital map. The RIA is a scalable platform that provides variable and adaptable feature modification for its users. It is also designed to incorporate different layers of knowledge to allow selective viewing to protect sensitive indigenous biodiversity data. The use of spatial information will enable researcher to analyze ecological trends and behavior. The RIA is also accessible via the web for easy data population and curation. Future funedit
... zafril@ump.edu.my, kamarul@fsksm.utm.my, hanan@fsksm.utm.my, shahir@fbb.utm.my, safawati@ump.edu.my Abstract ... Heidelberg, Germany : Springer-Verlag, Lecture Notes in Computer Science, 2007. [8] A. Rasooli, M. Mirza-Aghatabar and S.... more
... zafril@ump.edu.my, kamarul@fsksm.utm.my, hanan@fsksm.utm.my, shahir@fbb.utm.my, safawati@ump.edu.my Abstract ... Heidelberg, Germany : Springer-Verlag, Lecture Notes in Computer Science, 2007. [8] A. Rasooli, M. Mirza-Aghatabar and S. Khorsandi. ...
Biodiversity informatics is a currently developing bioinformatics field that contributes to the management of the biodiversity and ecosystem by providing decision making cues to researchers, environmental managers and policymakers. It... more
Biodiversity informatics is a currently developing bioinformatics field that contributes to the management of the biodiversity and ecosystem by providing decision making cues to researchers, environmental managers and policymakers. It brings together ecologist, environmentalist and computer ...
... Shamsir, Mohd S. and Al-Hadi, Muhammad and Nik Wan, Nik Ahmad Firdaus Pembangunan Pengkalan Maklumat ... ini juga telah mendigitalkan peta analog untuk memudahkan rujukan para pengkaji seperti maklumat alam sekitar seperti ...... more
... Shamsir, Mohd S. and Al-Hadi, Muhammad and Nik Wan, Nik Ahmad Firdaus Pembangunan Pengkalan Maklumat ... ini juga telah mendigitalkan peta analog untuk memudahkan rujukan para pengkaji seperti maklumat alam sekitar seperti ... Deposited By: Mr Mohd Shahir Shamsir. ...
Biodiversity data is complex with different levels of data standard and quality. It also exists in non discrete data boundaries over a wide spectrum, from variation in genes to diversity of species within an ecosystem. Data sources and... more
Biodiversity data is complex with different levels of data standard and quality. It also exists in non discrete data boundaries over a wide spectrum, from variation in genes to diversity of species within an ecosystem. Data sources and collections are also very diverse as it is a mix of ...
When analysing a metabolic pathway through mathematical model, it is important that the significant parameters are being correctly estimated. However, this process often comes across problems such as easily being trapped in local minima,... more
When analysing a metabolic pathway through mathematical model, it is important that the significant parameters are being correctly estimated. However, this process often comes across problems such as easily being trapped in local minima, repetitive exposure to worse results during the search process, and occurrence of noisy data. Thus, an improved Bee Memory Differential Evolution algorithm (IBMDE), which is a hybrid of the Differential Evolution algorithm (DE), the Kalman Filter (KF), Artificial Bee Colony algorithm (ABC), and a memory feature is presented this paper. IBMDE is an improved estimation algorithm as previous work only utilised DE. The theronine biosynthesis pathway is the metabolic pathways used in this paper. For metabolite O-Phosphohomoserine production simulation, the IBMDE able to produce the estimated optimal kinetic parameter values with significantly reduced error rate (63.67%) and shows a faster convergence time (71.46%) compared to the Nelder Mead (NM), the Si...
Sperm-egg interaction defect is a significant cause of in-vitro fertilization failure for infertile cases. Numerous molecular interactions in the form of protein-protein interactions mediate the sperm-egg membrane interaction process.... more
Sperm-egg interaction defect is a significant cause of in-vitro fertilization failure for infertile cases. Numerous molecular interactions in the form of protein-protein interactions mediate the sperm-egg membrane interaction process. Recent studies have demonstrated that in addition to experimental techniques, computational methods, namely protein interaction network approach, can address protein-protein interactions between human sperm and egg. Up to now, no drugs have been detected to treat sperm-egg interaction disorder, and the initial step in drug discovery research is finding out essential proteins or drug targets for a biological process. The main purpose of this study is to identify putative drug targets for human sperm-egg interaction deficiency and consider if the detected essential proteins are targets for any known drugs using protein-protein interaction network and ingenuity pathway analysis. We have created human sperm-egg protein interaction networks with high confid...
In silico metabolic engineering interventions have received renewed attention due to the increase in the number of annotated genomes and the development of several genome-scale metabolic models. Using the retrosynthetic metabolic pathway... more
In silico metabolic engineering interventions have received renewed attention due to the increase in the number of annotated genomes and the development of several genome-scale metabolic models. Using the retrosynthetic metabolic pathway prediction method, we engineered metabolic strategies for the production of 1-butanol by Escherichia coli using the OptFlux software platform. The metabolic engineering model shows that the insertion of nucleotide sugar dehydrogenase enzyme from Leptothrix cholodnii is predicted to catalyse the production of 1-butanol in E. coli. The growth rate and the secretion profile of the mutant model was retained as the wild-type. The result demonstrates that the proposed engineered strain is capable of substantial butanol production increase when 1-butanol gene (nsdh/b3544) is overexpressed under semi-anaerobic conditions with fixed glucose and oxygen uptake rates of 8 mmol g DW–1 h–1 and 5 mmol g DW–1 h–1, respectively. We anticipate that our in silico resu...
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The use of genome-scale models of Escherichia coli to guide future metabolic engineering strategies for increased succinic acid production has received renewed attention in recent years. Substrate selectivity such as glycerol is of... more
The use of genome-scale models of Escherichia coli to guide future metabolic engineering strategies for increased succinic acid production has received renewed attention in recent years. Substrate selectivity such as glycerol is of particular interest, because it is currently generated as a by-product of biodiesel industry and therefore can serve as a solitary carbon source. However, study on the prediction of gene knockout candidates for enhanced succinate production from glycerol using Minimization of Metabolic Adjustment Algorithm with the OptFlux software platform remained underexplored. Here, we show that metabolic engineering interventions by gene knockout simulation of some pyruvate dissimilating pathway enzymes (lactate dehydrogenase A and pyruvate formate lyase A) using E. coli genome-scale model can reduce acetate flux and enhance succinic acid production under anaerobic conditions. The introduced genetic perturbations led to substantial improvement in succinate flux of ab...
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When analyzing a metabolic pathway in a mathematical model, it is important that the essential parameters are estimated correctly. However, this process often faces few problems like when the number of unknown parameters increase,... more
When analyzing a metabolic pathway in a mathematical model, it is important that the essential parameters are estimated correctly. However, this process often faces few problems like when the number of unknown parameters increase, trapping of data in the local minima, repeated exposure to bad results during the search process and occurrence of noisy data. Thus, this paper intends to present an improved bee memory differential evolution (IBMDE) algorithm to solve the mentioned problems. This is a hybrid algorithm that combines the differential evolution (DE) algorithm, the Kalman filter, artificial bee colony (ABC) algorithm, and a memory feature. The aspartate and threonine biosynthesis pathway, and cell cycle pathway are the metabolic pathways used in this paper. For three production simulation pathways, the IBMDE managed to robustly produce the estimated optimal kinetic parameter values with significantly reduced errors. Besides, it also demonstrated faster convergence time compar...
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ABSTRACT The process of analysing metabolic pathways mathematically in systems biology requires accurate parameters which represent the simulated in-vivo processes. Differential Evolution algorithm (DE) has been provenable to outperform... more
ABSTRACT The process of analysing metabolic pathways mathematically in systems biology requires accurate parameters which represent the simulated in-vivo processes. Differential Evolution algorithm (DE) has been provenable to outperform other estimation algorithms, and has been used to achieve an accurate estimation of the required parameters. The total number of DE-variants has increased recently, which makes researchers face difficulties in obtaining complete overview of current DE-variants. To provide a holistic view to the area of mathematical modelling in System Biology, through this paper, we present an overview of modelling methods, parameter estimation by utilizing DE-variants to analyse metabolic pathways, and exiting pathway simulation software.
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ABSTRACT The smartphones mobility and its pervasiveness are beginning to transform practices in biodiversity conservation. The integrated functionalities of a smartphone have created for the public and biodiversity specialists means to... more
ABSTRACT The smartphones mobility and its pervasiveness are beginning to transform practices in biodiversity conservation. The integrated functionalities of a smartphone have created for the public and biodiversity specialists means to identify, gather and record biodiversity data while simultaneously creating knowledge portability in the digital forms of mobile guides. Smartphones enable beginners to recreate the delight of species identification usually reserved for specialist with years of experience. Currently, the advent of Android platform has enabled stakeholders in biodiversity to harness the ubiquity of this platform and create various types of mobile application or "apps" for use in biodiversity research and conservation. However, there is an apparent lack of application devoted to the identification in herpetofauna or amphibian science. Amphibians are a large class of animals with many different species still unidentified under this category. Here we describe the development of an app called Amphibian Recognition Android Application (ARAA) to identify frog amphibian species as well as an accompanying field guide. The app has the amphibian taxonomic key which assists the users in easy and rapid species identification, thus facilitating the process of identification and recording of species occurrences in conservation work. We will also present an overview of the application work flow and how it is designed to meet the needs a conservationist. As this application is still in its beta phase, further research is required to improve the application to include tools such automatic geolocation and geotagging, participative sensing via crowdsourcing and automated identification via image capture. We believe that the introduction of this app will create an impetus to the awareness of nature via species identification.
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The Anoxybacillus sp. SK 3-4, previously isolated from a hot spring, was screened for its heavy metals resistance (Al(3+) , Mn(2+) , Cu(2+) , Co(2+) , Zn(2+) , and Ni(2+) ) and the strain was found to be most resistant to aluminum.... more
The Anoxybacillus sp. SK 3-4, previously isolated from a hot spring, was screened for its heavy metals resistance (Al(3+) , Mn(2+) , Cu(2+) , Co(2+) , Zn(2+) , and Ni(2+) ) and the strain was found to be most resistant to aluminum. Significant growth of the strain was observed when it was grown in medium containing aluminum (200 mg L(-1) -800 mg L(-1) ) with relative growth rates ranging between 77% and 100%. A gene encoding the aluminum resistance protein (accession number: WP_021095658.1) was found in genome of strain SK 3-4, which revealed high sequence identity (>95%) to its homologues from Anoxybacillus species. Sequence comparisons with two functionally characterized aluminum resistance proteins, namely G2alt and ALU1-P, showed 97% and 81% of sequence identity, respectively. Four putative metal binding sites were detected in SK 3-4 aluminum resistance protein and G2alt at same amino acid residue positions of 186, 195, 198, and 201. Strain SK 3-4 was found to be able to remo...
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The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best... more
The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and...
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ABSTRACT For simulation-based work, researchers often have limited hardware capacities and budgets, so they create a low-cost parallel computing platform using PCs and commodity hardware, assembled and configured as a Beowulf-class... more
ABSTRACT For simulation-based work, researchers often have limited hardware capacities and budgets, so they create a low-cost parallel computing platform using PCs and commodity hardware, assembled and configured as a Beowulf-class computing cluster. Here, an astute approach (for a molecular dynamics simulation example) greatly improves performance through hardware upgrades and other tricks.
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Abstract Our country imported rice to sustain demand from the public. In Malaysia 2 types of rice are grown; wetland rice which is widely cultivated while upland rice is cultivated on a smaller scale mostly by farmers in Sabah and... more
Abstract
Our country imported rice to sustain demand from the public. In Malaysia 2 types of rice are grown;
wetland rice which is widely cultivated while upland rice is cultivated on a smaller scale mostly by
farmers in Sabah and Sarawak. Through plant biotechnology, micropropagation method via tissue
culture and quantitative breeding traits are able to contribute to research on upland rice in Malaysia.
Prior to the establishment of efficient in vitro propagation of upland rice, study on embryogenic callus
induction is crucial. Our findings showed that NAA was not suitable for callus induction. Nevertheless,
the highest callus induction was observed when cultivars Wai (75%) and Panderas (90%) were cultured
on MSB5 media supplemented with 2 mg/L 2,4-D. Furthermore, addition of 20 g/L sorbitol had
increased callus induction of 70% and 80% for Wai and Panderas, respectively. In other assessment,
comparative study on ex vitro quantitative breeding trait showed that the height of plants without any
fertilizer treatment were higher than commercial EM-treated plant. Rice plant treated with EM
commercial soil had the shortest height and eventually died. However, rice planted with commercial
EM produced the highest number of grains per panicle, shorter maturity period as compared to control.
Keywords: Upland rice; embryogenic callus; quantitaive breeding trait; effective microorganisma
Abstrak
Malaysia mengimport sebahagian keperluan beras Negara bagi menampung permintaan beras yang
tinggi. Padi sawah ditanam secara meluas di Semenanjung Malaysia manakala padi bukit ditanam
secara kecil-kecilan oleh kebanyakanya petani di Sabah dan Sarawak. Pendekatan bioteknologi
tanaman, khususnya kaedah pembiakan mikro kultur tisu dan sifat pembiakan baka kuantitatif mampu
menyumbang kepada penyelidikan padi bukit di Malaysia. Sebelum kaedah pembiakan in vitro padi
bukit yang efisien dapat dibangunkan, kajian penginduksian kalus embriogeni adalah sangat penting.
Dalam kajian ini NAA didapati tidak sesuai dalam menginduksi kalus padi. Sejumlah 75%
penginduksian kalus dicerap bagi kultivar Wai manakala 90% bagi kultivar Panderas pada media
MSB5 yang ditambah 2 mg/L 2,4-D. Penambahan 20 g/L sorbitol Berjaya meningkatkan pertumbuhan
kalus untuk kultivar Wai dan Panderas masing-masing sebanyak 70% dan 80%. Kajian perbandingan
sifat pembiakan baka kuantitatif ex vitro mendapati semua jenis padi mempunyai ketinggian paling
tinggi bagi tanpa rawatan berbanding dengan rawatan baja komersil EM (mikroorganisma efektif). Padi
yang ditanam menggunakan baja tanah komersil EM mempunyai ketinggian paling rendah dan
akhirnya mati. Namun begitu, hasil padi menggunakan baja komersil EM mencatatkan jumlah biji
benih tertinggi serta mencapai hari matang yang lebih awal berbanding rawatan tanpa baja.
Kata kunci: Padi bukit; kalus embriogeni; sifat pembiakan kuantitatif; mikroorganisma efektif
Our country imported rice to sustain demand from the public. In Malaysia 2 types of rice are grown;
wetland rice which is widely cultivated while upland rice is cultivated on a smaller scale mostly by
farmers in Sabah and Sarawak. Through plant biotechnology, micropropagation method via tissue
culture and quantitative breeding traits are able to contribute to research on upland rice in Malaysia.
Prior to the establishment of efficient in vitro propagation of upland rice, study on embryogenic callus
induction is crucial. Our findings showed that NAA was not suitable for callus induction. Nevertheless,
the highest callus induction was observed when cultivars Wai (75%) and Panderas (90%) were cultured
on MSB5 media supplemented with 2 mg/L 2,4-D. Furthermore, addition of 20 g/L sorbitol had
increased callus induction of 70% and 80% for Wai and Panderas, respectively. In other assessment,
comparative study on ex vitro quantitative breeding trait showed that the height of plants without any
fertilizer treatment were higher than commercial EM-treated plant. Rice plant treated with EM
commercial soil had the shortest height and eventually died. However, rice planted with commercial
EM produced the highest number of grains per panicle, shorter maturity period as compared to control.
Keywords: Upland rice; embryogenic callus; quantitaive breeding trait; effective microorganisma
Abstrak
Malaysia mengimport sebahagian keperluan beras Negara bagi menampung permintaan beras yang
tinggi. Padi sawah ditanam secara meluas di Semenanjung Malaysia manakala padi bukit ditanam
secara kecil-kecilan oleh kebanyakanya petani di Sabah dan Sarawak. Pendekatan bioteknologi
tanaman, khususnya kaedah pembiakan mikro kultur tisu dan sifat pembiakan baka kuantitatif mampu
menyumbang kepada penyelidikan padi bukit di Malaysia. Sebelum kaedah pembiakan in vitro padi
bukit yang efisien dapat dibangunkan, kajian penginduksian kalus embriogeni adalah sangat penting.
Dalam kajian ini NAA didapati tidak sesuai dalam menginduksi kalus padi. Sejumlah 75%
penginduksian kalus dicerap bagi kultivar Wai manakala 90% bagi kultivar Panderas pada media
MSB5 yang ditambah 2 mg/L 2,4-D. Penambahan 20 g/L sorbitol Berjaya meningkatkan pertumbuhan
kalus untuk kultivar Wai dan Panderas masing-masing sebanyak 70% dan 80%. Kajian perbandingan
sifat pembiakan baka kuantitatif ex vitro mendapati semua jenis padi mempunyai ketinggian paling
tinggi bagi tanpa rawatan berbanding dengan rawatan baja komersil EM (mikroorganisma efektif). Padi
yang ditanam menggunakan baja tanah komersil EM mempunyai ketinggian paling rendah dan
akhirnya mati. Namun begitu, hasil padi menggunakan baja komersil EM mencatatkan jumlah biji
benih tertinggi serta mencapai hari matang yang lebih awal berbanding rawatan tanpa baja.
Kata kunci: Padi bukit; kalus embriogeni; sifat pembiakan kuantitatif; mikroorganisma efektif
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Elucidation of the sperm-egg interaction at the molecular level is one of the unresolved problems in sexual reproduction, and understanding the molecular mechanism is crucial in solving problems in infertility and failed in vitro... more
Elucidation of the sperm-egg interaction at the molecular level is one of the unresolved problems in sexual reproduction, and understanding the molecular mechanism is crucial in solving problems in infertility and failed in vitro fertilization (IVF). Many molecular interactions in the form of protein-protein interactions (PPIs) mediate the sperm-egg membrane interaction. Due to the complexity of the problem such as difficulties in analyzing in vivo membrane PPIs, many efforts have failed to comprehensively elucidate the fusion mechanism and the molecular interactions that mediate sperm-egg membrane fusion. The main purpose of this study was to reveal possible protein interactions and associated molecular function during sperm-egg interaction using a protein interaction network approach. Different databases have been used to construct the human sperm-egg interaction network. The constructed network revealed new interactions. These included CD151 and CD9 in human oocyte that interact with CD49 in sperm, and CD49 and ITGA4 in sperm that interact with CD63 and CD81, respectively, in the oocyte. These results showed that the different integrins in sperm may be involved in human sperm-egg interaction. It was also suggested that sperm ADAM2 plays a role as a protein candidate involved in sperm-egg membrane interaction by interacting with CD9 in the oocyte. Interleukin-4 receptor activity, receptor signaling protein tyrosine kinase activity, and manganese ion transmembrane transport activity are the major molecular functions in sperm-egg interaction protein network. The disease association analysis indicated that sperm-egg interaction defects are also reflected in other disease networks such as cardiovascular, hematological, and breast cancer diseases. By analyzing the network, we identified the major molecular functions and disease association genes in sperm-egg interaction protein. Further experimental studies will be required to confirm the significance of these new computationally resolved interactions and the genetic links between sperm-egg interaction abnormalities and the associated disease.
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Abstract: Currently, all information regarding rice research in Malaysia are scattered over many different publications, depositories and databases using various digital and analogue formats. Although several international databases of... more
Abstract: Currently, all information regarding rice research in Malaysia are scattered over many different publications, depositories and databases using various digital and analogue formats. Although several international databases of rice research are available, they are not linked to geolocation and other basic archival information. We present MyRice; a systematic Malaysian online rice knowledge database for researchers and citizen scientists to curate their data. The creation of this database will enable scientific researchers to trace back rice research information and their locality effectively. It is constructed using a digitization pipeline that allow high throughput digitization of archival data and connected with publication search engine such as Google Scholar. The main functions include bibliography, map locational visualization and media uploader to share videos and images. We believe that MyRice will contribute to the digital knowledge ecosystem among rice researchers to elevate access and become a focal point for driving Malaysian rice research towards a sulf-sufficient country on food security. The database is available http://biodiversity.fbb.utm.my/myrice/.
Abstrak: Pada masa ini, semua maklumat mengenai penyelidikan padi di Malaysia bertaburan di penerbitan yang berbeza, depositori dan pangkalan data dengan menggunakan pelbagai format digital dan analog. Walaupun terdapat pangkalan data antarabangsa mengenai penyelidikan padi, data tersebut tidak dipautkan dengan dengan geolokasi dan maklumat arkib asas lain yang diperlukan penyelidik untuk membawa penyelidikan ke peringkat yang lebih tinggi. Kami mempersembahkan MyRice, sebuah pangkalan data atas talian Malaysia untuk kegunaan penyelidik dan orang awam. Pembangunan pangkalan data ini akan membolehkan penyelidik saintifik untuk mengesan kembali maklumat penyelidikan padi dan lokasi ia ditanam. Ia dibina menggunakan saluran pendigitalan yang membolehkan pendigitalan pemprosesan berkelajuan tinggi data arkib dan dihubungkan terus dengan enjin carian penerbitan seperti Google Scholar. Fungsi utama termasuk bibliografi, pemetaan dan pemuat naik media untuk penyelidik berkongsi video dan imej. Kami percaya MyRice yang akan menyumbang kepada ekosistem pengetahuan digital di kalangan penyelidik padi tempatan untuk meningkatkan akses kepada pengetahuan dan menjadi tumpuan utama untuk memacu penyelidikan padi Malaysia ke arah sebuah negara berstatus sara diri dalam keterjaminan makanan. Pangkalan data dapat dilayari di http://biodiversity.fbb.utm.my/myrice/.
Abstrak: Pada masa ini, semua maklumat mengenai penyelidikan padi di Malaysia bertaburan di penerbitan yang berbeza, depositori dan pangkalan data dengan menggunakan pelbagai format digital dan analog. Walaupun terdapat pangkalan data antarabangsa mengenai penyelidikan padi, data tersebut tidak dipautkan dengan dengan geolokasi dan maklumat arkib asas lain yang diperlukan penyelidik untuk membawa penyelidikan ke peringkat yang lebih tinggi. Kami mempersembahkan MyRice, sebuah pangkalan data atas talian Malaysia untuk kegunaan penyelidik dan orang awam. Pembangunan pangkalan data ini akan membolehkan penyelidik saintifik untuk mengesan kembali maklumat penyelidikan padi dan lokasi ia ditanam. Ia dibina menggunakan saluran pendigitalan yang membolehkan pendigitalan pemprosesan berkelajuan tinggi data arkib dan dihubungkan terus dengan enjin carian penerbitan seperti Google Scholar. Fungsi utama termasuk bibliografi, pemetaan dan pemuat naik media untuk penyelidik berkongsi video dan imej. Kami percaya MyRice yang akan menyumbang kepada ekosistem pengetahuan digital di kalangan penyelidik padi tempatan untuk meningkatkan akses kepada pengetahuan dan menjadi tumpuan utama untuk memacu penyelidikan padi Malaysia ke arah sebuah negara berstatus sara diri dalam keterjaminan makanan. Pangkalan data dapat dilayari di http://biodiversity.fbb.utm.my/myrice/.
Research Interests:
Currently, all the information regarding ethnobotanical, phytochemical and pharmaceutical information of South East Asia are scattered over many different publications, depositories and databases using various digital and analogue... more
Currently, all the information regarding ethnobotanical, phytochemical and pharmaceutical information of South East Asia are scattered over many different publications, depositories and databases using various digital and analogue formats. Although there are taxonomic databases of medicinal plants, they are not linked to phytochemical and pharmaceutical information which are often resides in scientific literature. We present Phyknome; an ethnobotanical and phytochemical database with more than 22,000 species of ethnoflora of Asia. The creation of this database will enable a biotechnology researcher to seek and identify ethnobotanical information based on a species’ scientific name, description and phytochemical information. It is constructed using a digitization pipeline that allow high throughput digitization of archival data, an automated dataminer to mine for pharmaceutical compounds information and an online database to integrated these information. The main functions include an automated taxonomy, bibliography and API interface with primary databases such as Global Biodiversity Information Facility (GBIF). We believe that Phyknome will contribute to the digital knowledge ecosystem to elevate access and provide tools for ethnobotanical research and contributes to the management, assessment and stewardship of biodiversity. The database is available at http://mapping.fbb.utm.my/phyknome/.
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Several visualization tools for the mapping of protein-protein interactions have been developed in recent years. However, a systematic comparison of the virtues and limitations of different PPI visualization tools has not been carried out... more
Several visualization tools for the mapping of protein-protein interactions have been developed in recent years. However, a systematic comparison of the virtues and limitations of different PPI visualization tools has not been carried out so far. In this study, we compare seven commonly used visualization tools, based on input and output file format, layout algorithm, database integration, Gene Ontology annotation and accessibility of each tool. The assessment was carried out based on brain disease datasets. Our suggested tools, NAViGaTOR, Cytoscape and Gephi perform competitively as PPI network visualization tools, can be a reference for future researches on PPI mapping and analysis.
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A novel α-amylase was isolated successfully from Glaciozyma antarctica PI12 using DNA walking and reverse transcription-polymerase chain reaction (RT-PCR) methods. The structure of this psychrophilic α-amylase (AmyPI12) from G. antarctica... more
A novel α-amylase was isolated successfully from Glaciozyma antarctica PI12 using DNA walking and reverse transcription-polymerase chain reaction (RT-PCR) methods. The structure of this psychrophilic α-amylase (AmyPI12) from G. antarctica PI12 has yet to be studied in detail. A 3D model of AmyPI12 was built using a homology modelling approach to search for a suitable template and to generate an optimum target–template alignment, followed by model building using MODELLER9.9. Analysis of the AmyPI12 model revealed the presence of binding sites for a conserved calcium ion (CaI), non-conserved calcium ions (CaII and CaIII) and a sodium ion (Na). Compared with its template—the thermostable α-amylase from Bacillus stearothermophilus (BSTA)—the binding of CaII, CaIII and Na ions in AmyPI12 was observed to be looser, which suggests that the low stability of AmyPI12 allows the protein to work at different temperature scales. The AmyPI12 amino acid sequence and model were compared with thermophilic α-amylases from Bacillus species that provided the highest structural similarities with AmyPI12. These comparative studies will enable identification of possible determinants of cold adaptation.
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The structure of psychrophilic chitinase (CHI II) from Glaciozyma antarctica PI12 has yet to be studied in detail. Due to its low sequence identity (<30 %), the structural prediction of CHI II is a challenge. A 3D model of CHI II was... more
The structure of psychrophilic chitinase (CHI II) from Glaciozyma antarctica PI12 has yet to be studied in detail. Due to its low sequence identity (<30 %), the structural prediction of CHI II is a challenge. A 3D model of CHI II was built by first using a threading approach to search for a suitable template and to generate an optimum target-template alignment, followed by model building using MODELLER9v7. Analysis of the catalytic insertion domain structure in CHI II revealed an increase in the number of aromatic residues and longer loops compared to mesophilic and thermophilic chitinases. A molecular dynamics simulation was used to examine the stability of the CHI II structure at 273, 288 and 300 K. Structural analysis of the substrate-binding cleft revealed a few exposed aromatic residues. Substitutions of certain amino acids in the surface and loop regions of CHI II conferred an increased flexibility to the enzyme, allowing for an adaptation to cold temperatures. A substrate binding comparison of CHI II with the mesophilic chitinase from Coccidioides immitis, 1D2K, suggested that the psychrophilic adaptation and catalytic activity at low temperatures were achieved through a reduction in the number of salt bridges, fewer hydrogen bonds and an increase in the exposure of the hydrophobic side chains to the solvent.
Research Interests: Bioinformatics, Molecular Dynamics Simulation, Genomics, Protein Structure Prediction, Proteomics, and 8 moreCancer Biology, Transcription Factors, Next generation sequencing, Chitinases,cellulases and Glucanases by Trichoderma, Biomolecular Modeling, Psychrophilic, Self assembly of Macromolecules, and Gene expression and regulation
We present the development of a web server, a protein short motif search tool that allows users to simultaneously search for a protein sequence motif and its secondary structure assignments. The web server is able to query very short... more
We present the development of a web server, a protein short motif search tool that allows users to simultaneously search for a protein sequence motif and its secondary structure assignments. The web server is able to query very short motifs searches against PDB structural data from the RCSB Protein Databank, with the users defining the type of secondary structures of the amino acids in the sequence motif. The output utilises 3D visualisation ability that highlights the position of the motif in the structure and on the corresponding sequence. Researchers can easily observe the locations and conformation of multiple motifs among the results. Protein short motif search also has an application programming interface (API) for interfacing with other bioinformatics tools.