An Integrated System at the Bleien Observatory for Mapping the Galaxy

We describe the design and performance of the hardware system at the Bleien Observatory. The system is designed to deliver a map of the Galaxy for studying the foreground contamination of low-redshift (z=0.13--0.43) H$_{\rm I}$ intensity mapping experiments as well as other astronomical Galactic studies. This hardware system is composed of a 7m parabolic dish, a dual-polarization corrugated horn feed, a pseudo correlation receiver, a Fast Fourier Transform spectrometer, and an integrated control system that controls and monitors the progress of the data collection. The main innovative designs in the hardware are (1) the pseudo correlation receiver and the cold reference source within (2) the high dynamic range, high frequency resolution spectrometer and (3) the phase-switch implementation of the system. This is the first time these technologies are used together for a L-band radio telescope to achieve an electronically stable system, which is an essential first step for wide-field cosmological measurements. This work demonstrates the prospects and challenges for future H$_{\rm I}$ intensity mapping experiments.Comment: 11 pages, 12 figures, 1 table, Submitted to MNRA

RJPrimers: unique transposable element insertion junction discovery and PCR primer design for marker development

Transposable elements (TE) exist in the genomes of nearly all eukaryotes. TE mobilization through ‘cut-and-paste’ or ‘copy-and-paste’ mechanisms causes their insertions into other repetitive sequences, gene loci and other DNA. An insertion of a TE commonly creates a unique TE junction in the genome. TE junctions are also randomly distributed along chromosomes and therefore useful for genome-wide marker development. Several TE-based marker systems have been developed and applied to genetic diversity assays, and to genetic and physical mapping. A software tool ‘RJPrimers’ reported here allows for accurate identification of unique repeat junctions using BLASTN against annotated repeat databases and a repeat junction finding algorithm, and then for fully automated high-throughput repeat junction-based primer design using Primer3 and BatchPrimer3. The software was tested using the rice genome and genomic sequences of Aegilops tauschii. Over 90% of repeat junction primers designed by RJPrimers were unique. At least one RJM marker per 10 Kb sequence of A. tauschii was expected with an estimate of over 0.45 million such markers in a genome of 4.02 Gb, providing an almost unlimited source of molecular markers for mapping large and complex genomes. A web-based server and a command line-based pipeline for RJPrimers are both available at http://wheat.pw.usda.gov/demos/RJPrimers/

ASePCR: alternative splicing electronic RT–PCR in multiple tissues and organs

RT–PCR is one of the most powerful and direct methods to detect transcript variants due to alternative splicing (AS) that increase transcript diversity significantly in vertebrates. ASePCR is an efficient web-based application that emulates RT–PCR in various tissues. It estimates the amplicon size for a given primer pair based on the transcript models identified by the reverse e-PCR program of the NCBI. The tissue specificity of each PCR band is deduced from the tissue information of expressed sequence tag (EST) sequences compatible with each transcript structure. The output page shows PCR bands like a gel electrophoresis in various tissues. Each band in the output picture represents a putative isoform that could happen in a tissue-specific manner. It also shows the EST alignment and tissue information in the genome browser. Furthermore, the user can compare the AS patterns of orthologous genes in other species. The ASePCR, available at , supports the transcriptome models of the RefSeq, Ensembl, ECgene and AceView for human, mouse, rat and chicken genomes. It will be a valuable web resource to explore the transcriptome diversity associated with different tissues and organs in multiple species

Security, Trust and Privacy (STP) Model for Federated Identity and Access Management (FIAM) Systems

The federated identity and access management systems facilitate the home domain organization users to access multiple resources (services) in the foreign domain organization by web single sign-on facility. In federated environment the user’s authentication is performed in the beginning of an authentication session and allowed to access multiple resources (services) until the current session is active. In current federated identity and access management systems the main security concerns are: (1) In home domain organization machine platforms bidirectional integrity measurement is not exist, (2) Integrated authentication (i.e., username/password and home domain machine platforms mutual attestation) is not present and (3) The resource (service) authorization in the foreign domain organization is not via the home domain machine platforms bidirectional attestation

Implementing a digital infrastructure for the lab using a central laboratory server and the SiLA2 communication standard

In this report, a fully integrated solution for laboratory digitization is presented. The approach presents a flexible and complete integration method for the digitally assisted workflow. The worker in the laboratory performs procedures in direct interaction with the digitized infrastructure that guides through the process and aids while performing tasks. The digital transformation of the laboratory starts with standardized integration of both new and “smart” lab devices, as well as legacy devices through a hardware gateway module. The open source Standardization in Lab Automation 2 standard is used for device communication. A central lab server channels all device communication and keeps a database record of every measurement, task and result generated or used in the lab. It acts as a central entry point for process management. This backbone enables a process control system to guide the worker through the lab process and provide additional assistance, like results of automated calculations or safety information. The description of the infrastructure and architecture is followed by a practical example on how to implement a digitized workflow. This approach is highly useful for – but not limited to – the biotechnological laboratory and has the potential to increase productivity in both industry and research for example by enabling automated documentation

Forensic information management system

The primary objectives of this project were to reduce the paper work, increase data reliability and reduce process turnaround time at the West Virginia State Police Forensic Laboratory (WVSPFL) Charleston, WV. The objective was achieved by reengineering and automating various processes in the seven units of the laboratory. A software tool called Forensic Information Management System (FIMS) was developed. FIMS was implemented in Visual Studio.Net; MS-SQL server was used as the database. The FIMS can be accessed via the internet/intranet, Personal Digital Assistant (PDA), or a stand-alone desktop computer. The key benefits of FIMS are its ability to integrate information flow, information exchange between Originating (ORI) agencies, track the status of cases submitted to WVSPFL, report generation and directly uploading of data to the Laboratory Information Management System (LIMS)

Secure entity authentication

According to Wikipedia, authentication is the act of confirming the truth of an attribute of a single piece of a datum claimed true by an entity. Specifically, entity authentication is the process by which an agent in a distributed system gains confidence in the identity of a communicating partner (Bellare et al.). Legacy password authentication is still the most popular one, however, it suffers from many limitations, such as hacking through social engineering techniques, dictionary attack or database leak. To address the security concerns in legacy password-based authentication, many new authentication factors are introduced, such as PINs (Personal Identification Numbers) delivered through out-of-band channels, human biometrics and hardware tokens. However, each of these authentication factors has its own inherent weaknesses and security limitations. For example, phishing is still effective even when using out-of-band-channels to deliver PINs (Personal Identification Numbers). In this dissertation, three types of secure entity authentication schemes are developed to alleviate the weaknesses and limitations of existing authentication mechanisms: (1) End user authentication scheme based on Network Round-Trip Time (NRTT) to complement location based authentication mechanisms; (2) Apache Hadoop authentication mechanism based on Trusted Platform Module (TPM) technology; and (3) Web server authentication mechanism for phishing detection with a new detection factor NRTT. In the first work, a new authentication factor based on NRTT is presented. Two research challenges (i.e., the secure measurement of NRTT and the network instabilities) are addressed to show that NRTT can be used to uniquely and securely identify login locations and hence can support location-based web authentication mechanisms. The experiments and analysis show that NRTT has superior usability, deploy-ability, security, and performance properties compared to the state-of-the-art web authentication factors. In the second work, departing from the Kerb eros-centric approach, an authentication framework for Hadoop that utilizes Trusted Platform Module (TPM) technology is proposed. It is proven that pushing the security down to the hardware level in conjunction with software techniques provides better protection over software only solutions. The proposed approach provides significant security guarantees against insider threats, which manipulate the execution environment without the consent of legitimate clients. Extensive experiments are conducted to validate the performance and the security properties of the proposed approach. Moreover, the correctness and the security guarantees are formally proved via Burrows-Abadi-Needham (BAN) logic. In the third work, together with a phishing victim identification algorithm, NRTT is used as a new phishing detection feature to improve the detection accuracy of existing phishing detection approaches. The state-of-art phishing detection methods fall into two categories: heuristics and blacklist. The experiments show that the combination of NRTT with existing heuristics can improve the overall detection accuracy while maintaining a low false positive rate. In the future, to develop a more robust and efficient phishing detection scheme, it is paramount for phishing detection approaches to carefully select the features that strike the right balance between detection accuracy and robustness in the face of potential manipulations. In addition, leveraging Deep Learning (DL) algorithms to improve the performance of phishing detection schemes could be a viable alternative to traditional machine learning algorithms (e.g., SVM, LR), especially when handling complex and large scale datasets