Genome mapping databases: data acquisition, storage and access.

The introduction of the genome database to the human gene mapping community in September 1990 heralded the advent of a new generation of databases to serve the needs of the human genome initiative over the coming years. The databases will act as a fulcrum around which the activities of the human genome initiative can be coordinated at an international level.     

Introducing a method for extracting horizontal migration patterns from data storage tags

While data storage tags typically provide information about depth and temperature, the horizontal position of fish is difficult to obtain. The objective of this study is therefore to introduce a method for reconstructing horizontal migration patterns of fish tagged with DSTs. The method works by: establishing a database on bathymetry and environmental information about the target area, moving a large number of virtual fish between the release and recapture positions using a biased random walk procedure, and then terminate trajectories where the information at position is in disagreement with the tag information. For example a trajectory is terminated if the tag depth is greater than the bottom depth. The method is exemplified with two tag recordings from Northeast Arctic cod (Gadus morhua L.) in the Barents Sea. The results show that termination of impossible trajectories limits the number of potential trajectories between release and recapture positions, and in particular the usage of multiple termination criteria (depth and temperature) proved to be effective in reducing the number of possible trajectories. The method is general, simple to use, and can also be used in combination with geolocation methods.     

A new computer method for the storage and manipulation of DNA gel reading data.

This paper describes a new way of storing DNA gel reading data and an accompanying set of computer programs. These programs will perform all the manipulations that are required on data gained by the so-called 'shotgun' method of DNA sequencing. This system simplifies the computer processing involved with this sequencing method and also has the capability of being able at any time during a project to display, lined up in register, all the gel reading covering any section of the sequence.     

Efficient TPA-based auditing scheme for secure cloud storage

In recent years, how to design efficient auditing protocol to verify the integrity of users’ data, which is stored in cloud services provider (CSP), becomes a research focus. Homomorphic message authentication code (MAC) and homomorphic signature are two popular techniques to respectively design private and public auditing protocols. On the one hand, it is not suitable for the homomorphic-MAC-based auditing protocols to be outsourced to third-party auditor (TPA), who has more professional knowledge and computational abilities, although they have high efficiencies. On the other hand, the homomorphic-signature-based ones are very suitable for employing TPA without compromising user’s signing key but have very low efficiency (compared to the former case). In this paper, we propose a new auditing protocol, which perfectly combines the advantages of above two cases. In particular, it is almost as efficient as a homomorphic-MAC-based protocol proposed by Zhang et al. recently. Moreover, it is also suitable for outsourcing to TPA because it does not compromise the privacy of users’ signing key, which can be seen from our security analysis. Finally, numerical analysis and experimental results demonstrate the high-efficiency of our protocol.

     

Data storage and data re-use in taxonomy—the need for improved storage and accessibility of heterogeneous data

The ability to rapidly generate and share molecular, visual, and acoustic data, and to compare them with existing information, and thereby to detect and na     

A compressed sensing based approach for subtyping of leukemia from gene expression data

With the development of genomic techniques, the demand for new methods that can handle high-throughput genome-wide data effectively is becoming stronger than ever before. Compressed sensing (CS) is an emerging approach in statistics and signal processing. With the CS theory, a signal can be uniquely reconstructed or approximated from its sparse representations, which can therefore better distinguish different types of signals. However, the application of CS approach to genome-wide data analysis has been rarely investigated. We propose a novel CS-based approach for genomic data classification and test its performance in the subtyping of leukemia through gene expression analysis. The detection of subtypes of cancers such as leukemia according to different genetic markups is significant, which holds promise for the individualization of therapies and improvement of treatments. In our work, four statistical features were employed to select significant genes for the classification. With our selected genes out of 7,129 ones, the proposed CS method achieved a classification accuracy of 97.4% when evaluated with the cross validation and 94.3% when evaluated with another independent data set. The robustness of the method to noise was also tested, giving good performance. Therefore, this work demonstrates that the CS method can effectively detect subtypes of leukemia, implying improved accuracy of diagnosis of leukemia.     

SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis

We have compared the accuracy, efficiency and robustness of three methods of genotyping single nucleotide polymorphisms on pooled DNAs. We conclude that (i) the frequencies of the two alleles in pools should be corrected with a factor for unequal allelic amplification, which should be estimated from the mean ratio of a set of heterozygotes (k); (ii) the repeatability of an assay is more important than pinpoint accuracy when estimating allele frequencies, and assays should therefore be optimised to increase the repeatability; and (iii) the size of a pool has a relatively small effect on the accuracy of allele frequency estimation. We therefore recommend that large pools are genotyped and replicated a minimum of four times. In addition, we describe statistical approaches to allow rigorous comparison of DNA pool results. Finally, we describe an extension to our ACeDB database that facilitates management and analysis of the data generated by association studies.     

Efficient and inexpensive method for purification of heparin binding proteins

Heparin binding (HB) proteins mediate a wide range of important cellular processes, which makes this class of proteins biopharmaceutically important. Engineering HB proteins may bring many advantages, but it necessitates cost effective and efficient purification methodologies compared to currently available methods. One of the most important classes of HB proteins are fibroblast growth factors (FGFs) and their receptors (FGFRs). In this study, we report an efficient off-column purification of FGF-1 from soluble fractions and purification of the D2 domain of FGFR from insoluble inclusion bodies, using a weak Amberlite cation (IRC) exchanger. FGF-1 and the D2 domain have been expressed in Escherichia coli and purified to homogeneity using IRC resin. This approach is an alternative to conventional affinity column chromatography, which exhibits several disadvantages, including time-consuming experimental procedures for purification and regeneration and results in the expensive production of recombinant proteins. Results of the heparin binding chromatography and steady state fluorescence experiments show that the FGF-1 and the D2 are in a native conformation. The findings of this study will not only aid an in-depth investigation of this class of proteins but will also provide avenues for inexpensive and efficient purification of other important biological macromolecules.     

基于地面观测的陆地生态系统碳储量多源数据整合方法

陆地生态系统有机碳储量通常指一定面积的植被、土壤和凋落物的有机碳存储量总和。准确评估陆地生态系统碳储量现状和变化,对于揭示全球变化对陆地生态系统碳库的影响、指导政府决策者制定气候应对策略和评估现有措施的有效性等具有重要意义。地面观测数据是生态系统碳储量及其变化评估的重要数据源之一,但目前除少数生态站开展了长期地面数据观测外,绝大多数地面观测数据呈现出多源化、相互不匹配、时间不连续等特点;因此,迫切需要发展科学、规范化的多源数据整合方法,将这些多源、分散的地面观测数据整编形成长期系统的地面动态观测数据集,提高数据资源价值。从陆地生态系统碳储量组分及其基本算法着手,系统梳理了植被和土壤碳储量估算中植被不同器官生物量和碳含量、土壤碳含量、土壤容重等关键参数的观测现状,并详细介绍了这些关键参数的科学推导方法。此外,也进一步讨论了多源地面观测碳储量数据整合的方法,并展望了该方法体系未来的发展方向,期待能为后续相关研究提供可借鉴的规范性方法。