Educating the educators: Incorporating bioinformatics into biological science education in Malaysia

Bioinformatics can be defined as a fusion of computational and biological sciences. The urgency to process and analyse the deluge of data created by proteomics and genomics studies has caused bioinformatics to gain prominence and importance. However, its multidisciplinary nature has created a unique demand for specialist trained in both biology and computing. In this review, we described the components that constitute the bioinformatics field and distinctive education criteria that are required to produce individuals with bioinformatics training. This paper will also provide an introduction and overview of bioinformatics in Malaysia. The existing bioinformatics scenario in Malaysia was surveyed to gauge its advancement and to plan for future bioinformatics education strategies. For comparison, we surveyed methods and strategies used in education by other countries so that lessons can be learnt to further improve the implementation of bioinformatics in Malaysia. It is believed that accurate and sufficient steerage from the academia and industry will enable Malaysia to produce quality bioinformaticians in the future

Guest editorial : In Journal of networks, v.7 n.3

Networking of computing devices has been going through rapid evolution and thus continuing to be an ever expanding area of importance in recent years. New technologies, protocols, services and usage patterns have contributed to the major research interests in this area of computer science. The current special issue is an effort to bring forward some of these interesting developments that are being pursued by researchers at present in different parts of the globe. Our objective is to provide the readership with some insight into the latest innovations in computer networking through this. This Special Issue presents selected papers from the thirteenth conference of the series (ICCIT 2010) held during December 23-25, 2010 at the Ahsanullah University of Science and Technology. The first ICCIT was held in Dhaka, Bangladesh, in 1998. Since then the conference has grown to be one of the largest computer and IT related research conferences in the South Asian region, with participation of academics and researchers from many countries around the world. Starting in 2008 the proceedings of ICCIT are included in IEEExplore. In 2010, a total of 410 full papers were submitted to the conference of which 136 were accepted after reviews conducted by an international program committee comprising 81 members from 16 countries. This was tantamount to an acceptance rate of 33%. From these 136 papers, 14 highly ranked manuscripts were invited for this Special Issue. The authors were advised to enhance their papers significantly and submit them to undergo review for suitability of inclusion into this publication. Of those, eight papers survived the review process and have been selected for inclusion in this Special Issue. The authors of these papers represent academic and/or research institutions from Australia, Bangladesh, Japan, Korea and USA. These papers address issues concerning different domains of networks namely, optical fiber communication, wireless and interconnection networks, issues related to networking hardware and software and network mobility. The paper titled “Virtualization in Wireless Sensor Network: Challenges and Opportunities” argues in favor of bringing in different heterogeneous sensors under a common virtual framework so that the issues like flexibility, diversity, management and security can be handled practically. The authors Md. Motaharul Islam and Eui-Num Huh propose an architecture for sensor virtualization. They also present the current status and the challenges and opportunities for further research on the topic. The manuscript “Effect of Polarization Mode Dispersion on the BER Performance of Optical CDMA” deals with impact of polarization mode dispersion on the bit error rate performance of direct sequence optical code division multiple access. The authors, Md. Jahedul Islam and Md. Rafiqul Islam present an analytical approach toward determining the impact of different performance parameters. The authors show that the bit error rate performance improves significantly by the third order polarization mode dispersion than its first or second order counterparts. The authors Md. Shohrab Hossain, Mohammed Atiquzzaman and William Ivancic of the paper “Cost and Efficiency Analysis of NEMO Protocol Entities” present an analytical model for estimating the cost incurred by major mobility entities of a NEMO. The authors define a new metric for cost calculation in the process. Both the newly developed metric and the analytical model are likely to be useful to network engineers in estimating the resource requirement at the key entities while designing such a network. The article titled “A Highly Flexible LDPC Decoder using Hierarchical Quasi-Cyclic Matrix with Layered Permutation” deals with Low Density Parity Check decoders. The authors, Vikram Arkalgud Chandrasetty and Syed Mahfuzul Aziz propose a novel multi-level structured hierarchical matrix approach for generating codes of different lengths flexibly depending upon the requirement of the application. The manuscript “Analysis of Performance Limitations in Fiber Bragg Grating Based Optical Add-Drop Multiplexer due to Crosstalk” has been contributed by M. Mahiuddin and M. S. Islam. The paper proposes a new method of handling crosstalk with a fiber Bragg grating based optical add drop multiplexer (OADM). The authors show with an analytical model that different parameters improve using their proposed OADM. The paper “High Performance Hierarchical Torus Network Under Adverse Traffic Patterns” addresses issues related to hierarchical torus network (HTN) under adverse traffic patterns. The authors, M.M. Hafizur Rahman, Yukinori Sato, and Yasushi Inoguchi observe that dynamic communication performance of an HTN under adverse traffic conditions has not yet been addressed. The authors evaluate the performance of HTN for comparison with some other relevant networks. It is interesting to see that HTN outperforms these counterparts in terms of throughput and data transfer under adverse traffic. The manuscript titled “Dynamic Communication Performance Enhancement in Hierarchical Torus Network by Selection Algorithm” has been contributed by M.M. Hafizur Rahman, Yukinori Sato, and Yasushi Inoguchi. The authors introduce three simple adapting routing algorithms for efficient use of physical links and virtual channels in hierarchical torus network. The authors show that their approaches yield better performance for such networks. The final title “An Optimization Technique for Improved VoIP Performance over Wireless LAN” has been contributed by five authors, namely, Tamal Chakraborty, Atri Mukhopadhyay, Suman Bhunia, Iti Saha Misra and Salil K. Sanyal. The authors propose an optimization technique for configuring the parameters of the access points. In addition, they come up with an optimization mechanism in order to tune the threshold of active queue management system appropriately. Put together, the mechanisms improve the VoIP performance significantly under congestion. Finally, the Guest Editors would like to express their sincere gratitude to the 15 reviewers besides the guest editors themselves (Khalid M. Awan, Mukaddim Pathan, Ben Townsend, Morshed Chowdhury, Iftekhar Ahmad, Gour Karmakar, Shivali Goel, Hairulnizam Mahdin, Abdullah A Yusuf, Kashif Sattar, A.K.M. Azad, F. Rahman, Bahman Javadi, Abdelrahman Desoky, Lenin Mehedy) from several countries (Australia, Bangladesh, Japan, Pakistan, UK and USA) who have given immensely to this process. They have responded to the Guest Editors in the shortest possible time and dedicated their valuable time to ensure that the Special Issue contains high-quality papers with significant novelty and contributions

A review of Bennelongia De Deckker & McKenzie, 1981 (Crustacea, Ostracoda) species from eastern Australia with the description of three new species

Australia is predicted to have a high number of currently undescribed ostracod taxa. The genus Bennelongia De Deckker & McKenzie, 1981 (Crustacea, Ostracoda) occurs in Australia and New Zealand, and has recently shown potential for high speciosity, after the description of nine new species from Western Australia. Here, we focus on Bennelongia from eastern Australia, with the objectives of exploring likely habitats for undiscovered species, genetically characterising published morphological species and scanning classical species for cryptic diversity. Two traditional (morphological) species are confi rmed to be valid using molecular evidence (B. harpago De Deckker & McKenzie, 1981 and B. pinpi De Deckker, 1981), while three new species are described using both morphological and molecular evidence. Two of the new species belong to the B. barangaroo lineage (B. dedeckkeri sp. nov. and B. mckenziei sp. nov.), while the third is a member of the B. nimala lineage (B. regina sp. nov.). Another species was found to be genetically distinct, but is not formally described here owing to a lack of distinguishing morphological features from the existing species B. cuensis Martens et al., 2012. Trends in diversity and radiation of the genus are discussed, as well as implications these results have for the conservation of temporary pool microfauna and our understanding of Bennelongia’s evolutionary origin

Impact of sample preservation and manipulation on insect gut microbiome profiling : a test case with fruit flies (Diptera, Tephritidae)

High-throughput sequencing (HTS) techniques are of great value for the investigation of microbial communities, and have been extensively used to study the gut microbiome. While most studies focus on the human gut, many others have investigated insects. However, because of the rapid spread of HTS techniques, a lot of variation exists in the protocols for sample preparation. In the present study, we investigated the impact of two widely adopted sample-processing procedures preceding library preparation, i.e., preservation of insect tissue in 70% ethanol (EtOH) and sample dissection. We used the fruit fly Ceratitis capitata (Diptera: Tephritidae) as a model organism and set up two experiments, one comparing the effects of sample manipulation and preservation across life stages and the other across fruit samples from different sources. The results of this study showed no major effects of dissection on the outcome of HTS. However, EtOH preservation did have effects on the recovered gut microbiome, the main effect being a significant reduction of the dominant genus, Providencia, in EtOH-preserved samples. Less abundant bacterial groups were also affected resulting in altered microbial profiles obtained from samples preserved in 70% EtOH. These results have important implications for the planning of future studies and when comparing studies that used different sample preparation protocols

Strong approximations of level exceedences related to multiple hypothesis testing

Particularly in genomics, but also in other fields, it has become commonplace to undertake highly multiple Student's $t$-tests based on relatively small sample sizes. The literature on this topic is continually expanding, but the main approaches used to control the family-wise error rate and false discovery rate are still based on the assumption that the tests are independent. The independence condition is known to be false at the level of the joint distributions of the test statistics, but that does not necessarily mean, for the small significance levels involved in highly multiple hypothesis testing, that the assumption leads to major errors. In this paper, we give conditions under which the assumption of independence is valid. Specifically, we derive a strong approximation that closely links the level exceedences of a dependent ``studentized process'' to those of a process of independent random variables. Via this connection, it can be seen that in high-dimensional, low sample-size cases, provided the sample size diverges faster than the logarithm of the number of tests, the assumption of independent $t$-tests is often justified.Comment: Published in at http://dx.doi.org/10.3150/09-BEJ220 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm

BMICA-independent component analysis based on B-spline mutual information estimator

The information theoretic concept of mutual information provides a general framework to evaluate dependencies between variables. Its estimation however using B-Spline has not been used before in creating an approach for Independent Component Analysis. In this paper we present a B-Spline estimator for mutual information to find the independent components in mixed signals. Tested using electroencephalography (EEG) signals the resulting BMICA (B-Spline Mutual Information Independent Component Analysis) exhibits better performance than the standard Independent Component Analysis algorithms of FastICA, JADE, SOBI and EFICA in similar simulations. BMICA was found to be also more reliable than the 'renown' FastICA

Cloud Bioinformatics in a private cloud deployment

This chapter describes service portability for a private cloud deployment, including a detailed case study about Cloud Bioinformatics services developed as part of the Cloud Computing Adoption Framework (CCAF). The Cloud Bioinformatics design and deployment is based on Storage Area Network (SAN) technologies, details of which include functionalities, technical implementation, architecture, and user support. Bioinformatics applications are written on the SAN-based private cloud, which can simulate complex biological sciences and present them in a way that anyone without prior knowledge can understand. Several bioinformatics results are discussed, particularly brain segmentation, which demonstrates different parts of the brain simulated by the private cloud. In addition, benefits of CCAF are illustrated using several bioinformatics examples such as tumour modelling, brain imaging, insulin molecules, and simulations for medical training. The Cloud Bioinformatics solution offers cost reduction, time-saving, and user friendliness. </jats:p

An improved Plasmodium cynomolgi genome assembly reveals an unexpected methyltransferase gene expansion.

Background: Plasmodium cynomolgi, a non-human primate malaria parasite species, has been an important model parasite since its discovery in 1907. Similarities in the biology of P. cynomolgi to the closely related, but less tractable, human malaria parasite P. vivax make it the model parasite of choice for liver biology and vaccine studies pertinent to P. vivax malaria. Molecular and genome-scale studies of P. cynomolgi have relied on the current reference genome sequence, which remains highly fragmented with 1,649 unassigned scaffolds and little representation of the subtelomeres. Methods: Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated a new reference genome sequence, PcyM, sourced from an Indian rhesus monkey. We compare the newly assembled genome sequence with those of several other Plasmodium species, including a re-annotated P. coatneyi assembly. Results: The new PcyM genome assembly is of significantly higher quality than the existing reference, comprising only 56 pieces, no gaps and an improved average gene length. Detailed manual curation has ensured a comprehensive annotation of the genome with 6,632 genes, nearly 1,000 more than previously attributed to P. cynomolgi. The new assembly also has an improved representation of the subtelomeric regions, which account for nearly 40% of the sequence. Within the subtelomeres, we identified more than 1300 Plasmodium interspersed repeat (pir) genes, as well as a striking expansion of 36 methyltransferase pseudogenes that originated from a single copy on chromosome 9. Conclusions: The manually curated PcyM reference genome sequence is an important new resource for the malaria research community. The high quality and contiguity of the data have enabled the discovery of a novel expansion of methyltransferase in the subtelomeres, and illustrates the new comparative genomics capabilities that are being unlocked by complete reference genomes