Zeitschrift für Informatik und Systembiologie

The suffix ‘omics’ has been added to the names of many fields to denote studies undertaken on a large scale. Threshold science has become so pervasive in everyday life of making decisions. This paper provides a brief introduction and review to the emerging field of Threshnomics by explaining the threshold science applied in various domains. This paper reflects the wide range of threshold applications in algorithms and circuit design and attempt to correlate the threshold notion through neuronal equivalent operator.

Objective: Most bioinformatics applications that design primers for the technique of the PCR analyze one single sequence of DNA as template; only a few applications process various nucleotide sequences. A common feature of existing software is that produces primers that are unique for each template, which is partially useful in the genomic analysis. The objective was to create an application able to find the primers that are identical in multiple nucleotide sequences and the primers that are unique to each sequence.

Methods: I applied object-oriented programming using the C++ Builder 2009 to implement algorithms that find particular short strings (primers) in nucleotide sequences. The software is a set of applications with a simple design that serves as a didactic tool to find and analyze primers. To test the application, I used molecular biology to clone genes in the laboratory.

Results: I have developed a bioinformatics application for the PCR technology named SQPrimer that focus in finding identical primers in several sequences of nucleotides. I have shown the applicability and accuracy of the application in various examples of the genetic analysis. The software was able to 1: design primers at conserved sequences of nucleotides among different species; 2: find and design mutation specific primers in sequences with single nucleotide polymorphisms and 3: design primers to detect length polymorphisms: insertions, deletions or expansion of triplet nucleotide repeats.

Conclusion: SQPrimer is bioinformatics software that adds the capability of designing primers that are identical in a batch of sequences, a utility that can be used in some strategies of the PCR analysis. The software is accessible at http://www2.uah.es/biologia_celular/JPM/SQPP/SQPrimer.html.

Limited visibility in haze weather strongly influences the accuracy and the general functions of almost outdoor video surveillance or driver assistance systems. Actual weather condition is valuable information to invoke corresponding approaches. Based on the atmospheric scattering model analysis and the statistics of various outdoor images, for most foggy images, we find that the lowest and highest value in color channels tends to be the same value of atmospheric light. A function for estimating the haze degree is developed for the automatic detection of the foggy image with different haze degrees. Experimental results show that our haze classification method achieves high performance.

The omnidirectional mobile mechanism has high movement performance. We developed a prototype omnidirectional collision-detecting bumper using potentiometers for such a mobile mechanism. However, the previous prototype had low durability because it used contact-type sensors and a link mechanism to convert from the displacement of the bumper to the rotation of the potentiometers. In this paper, we propose a new prototype omnidirectional collision-detecting bumper using noncontact-type sensors. In an experiment, the new prototype showed higher accuracy than the previous one.

Currently, Internet has become a great database of knowledge and information for different disciplines. For instance, today, we can see the weather conditions for any place in any time online. All those data and information are important for geographic studies. However, transferring such information from Internet websites to GIS databases is a tides work. This paper presents an automatic approach to transfer Internet information to a GIS database using open source platform. The case study of Malaysia database is used to be updated with temperature data from Google engine by the developed application. The designed application is developed by DotSpatial platform and Visual Basic.Net programming environment. It consists of four modules: (a) connection to Google and search for temperature data. (b) The process module to process the inputs and calculate the HTML parameters. (c) Temperature data extraction module to find out the temperature data. (d) Shape file update module to append the temperature data into GIS database. The results of testing the developed application showed good results of updating the loaded shape file of Malaysia states with the temperature information.

Objective: To develop an automated 3D framework for prostate segmentation from diffusion-weighted imaging (DWI).

Methods: The proposed framework integrates level-set deformable model and nonnegative matrix factorization (NMF) techniques. In the proposed framework, the level-set is guided by a novel speed function that is derived using NMF, which extracts meaningful features from a large dimensional feature space. The NMF attributes are calculated using information from the DWI intensity, a probabilistic shape model, and the spatial interactions between prostate voxels. The shape model is constructed using a set of training prostate volumes and is then updated during the segmentation process using an appearance-based method that takes into account both a voxel’s location and its intensity value. The spatial interactions are modeled using a second-order pairwise 3D Markov-Gibbs random field (MGRF).

Results: We tested our framework on 125 in vivo DWI-MRI prostate data sets that has been collected from 10 subjects at b-values ranging from 0 to 1000 s/mm2. Our results show that using NMF-based feature fusion to guide the level-set increases the segmentation accuracy compared with previously proposed methods using two evaluation metrics, the dice similarity coefficient (DSC) and Hausdorff distance (HD). The proposed method achieved an average DSC of 0.868 ± 0.03 and an average HD of 5.61 ± 2.12 mm compared to an average DSC of 0.83±0.07 and an average HD of 6.67 ± 1.84 mm for a maximum a posteriori (MAP)-based level-set method, and an average DSC of 0.810 ± 0.05 and an average HD of 9.07 ± 1.64 for a level-set driven only by intensity and shape information.

Conclusions: Experimental results show that the integration of 3D intensity, shape, and spatial features with NMF-based feature fusion increases the ability of the proposed method to perform robust prostate segmentation despite image noise, inter-patient anatomical differences, and the similar intensities of the prostate and surrounding tissues.

Cancer is a broad term for a wide spectrum of diseases and which involves the alteration in expression levels of several hundreds of genes. As such, the study of the disease from a systems biology point of view becomes rational, as the properties of a system as a whole may be very different from the properties of its individual components. However, understanding a network at the systems level not only requires knowledge about the components of the network, but also the interactions between them. Here, a systems biology view of the rat PHD finger protein 5A (Phf5a) gene was attempted; a gene previously identified as aberrantly expressed in estrogen dependent endometrial adenocarcinoma tumors from both rat and human. Phf5ais a highly conserved cysteine rich (C4HC3) zinc finger and such proteins predominantly have a role in chromatin mediated transcriptional regulation. Moreover, PHF5A is a component of the macromolecular complex spliceosome that takes part in pre-mRNA splicing and spliceosome component coding genes have previously been shown to be implicated in various cancer types and suggested to potentially be novel antitumor drugs. To derive a systems biology view, in this study, a weighted gene network was inferred from a list of genes having correlated expression profiles to Phf5a as nodes, and common transcription factors and microRNAs regulating these genes together with annotation about biological process ontology term(s) and pathway(s) as edge weights. In the inferred network a higher weight indicates more annotation shared between two genes and, hence, the network facilitates the identification of closely interacting genes with Phf5a. The results show that highly weighted edges connect Phf5a to other spliceosome components, but also to genes involved in the metabolism of proteins, proteasome and DNA replication, repair and recombination. The results also link Phf5ato the Myc/Rb/E2F pathway, one of the central pathways associated with cancer. The proposed method for inferring a weighted gene network can easily be applied to other genes and diseases.

Objective: The existing informatics applications are specialized in particular aspects of the enzymatic restriction analysis of nucleotides sequences. In order to design an application that fulfills different needs of the investigation in restriction enzyme analysis, I have developed SQRestriction (SQR), a suite that compiles several utilities.

Methods: I applied object-oriented programming to set algorithms in C++ that compare the differences or similarities in the restriction sites of orthologous genes or in nucleotide sequences with single nucleotide polymorphisms, insertions or deletions.

Results: SQR is mainly a tool for the analysis of restriction fragment length polymorphisms but it has also other applications such as cloning of DNA; I demonstrate those functions in examples of different types of nucleotide sequences. I conducted a comparative analysis between SQR and existing software in the web; the main difference is that SQR is a suite of different applications that analyzes either one, two or multiple sequences of nucleotides.

Conclusion: I conclude that SQR is a competitive application since it offers differential features that are useful for academics and in laboratories of molecular biology. The SQRestriction software is open access at http://www2.uah.es/biologia_celular/JPM/SQR/SQR.html

In current scenario, microsatellites are a large source of genetic markers. In this study, we mined simple sequence repeats in whole genome of Xanthomonas species (Xanthomonas axonopodis pv. citri, Xanthomonas oryzae pv. oryzae, Xanthomonas campestris pv. Campestris) by in silico methods. A total of 640 SSRs, 377 SSRs and 541 SSRs were detected in whole genome having density of 1SSR/8.08 kb, 1SSR/13.10 kb and 1SSR/9.510 kb for 5175.554 kb, 4941.439 kb and 5148.708 kb sequences length respectively. The results elucidated, only 32 types (0.618%), 39 types (0.789%) and 96 types (1.864%) of SSR sequences were present in Xanthomonas axonopodis pv. citri, Xanthomonas oryzae pv.oryzae and Xanthomonas campestris pv. campestis respectively. Depending on the repeat units, the length of SSRs ranged from 10 to 18 bp for di-, 12 to 27 bp for tri-, 12 to 24 bp for tetra-, 20 to 35 bp for penta-, 24 to 72 for hexa-, 21 to 133 bp for hepta-, 24 to 40 bp for octa- and 27 to 36 bp for nano nucleotide repeats. Di-nucleotide repeats were the most frequent repeat type (70.97%) followed by tri-nucleotide (22.23%), hepta–nucleotide (2.86%), hexa-nucleotide (1.91%) and tetra-nucleotide (1.392%) in all three species of Xanthomonas. Annotation of sequences containing SSRs were also carried out to assign function to each of the sequences. SSR containing sequences of Xanthomonas species could not assign any specific class of protein (77.56%) due to the absence of homologs in the protein sequence database and these could be treated as an ideal molecular marker.