Network Traffic Anomaly Detection via Deep Learning

Network intrusion detection is a key pillar towards the sustainability and normal operation of information systems. Complex threat patterns and malicious actors are able to cause severe damages to cyber-systems. In this work, we propose novel Deep Learning formulations for detecting threats and alerts on network logs that were acquired by pfSense, an open-source software that acts as firewall on FreeBSD operating system. pfSense integrates several powerful security services such as firewall, URL filtering, and virtual private networking among others. The main goal of this study is to analyse the logs that were acquired by a local installation of pfSense software, in order to provide a powerful and efficient solution that controls traffic flow based on patterns that are automatically learnt via the proposed, challenging DL architectures. For this purpose, we exploit the Convolutional Neural Networks (CNNs), and the Long Short Term Memory Networks (LSTMs) in order to construct robust multi-class classifiers, able to assign each new network log instance that reaches our system into its corresponding category. The performance of our scheme is evaluated by conducting several quantitative experiments, and by comparing to state-of-the-art formulations.

The Propagation and Interaction of Supraharmonics from Electric Vehicle Chargers in a Low-Voltage Grid

The recent increase in large converter-based devices like electric vehicles and photovoltaics increases supraharmonic emissions in low-voltage grids, potentially affecting customer equipment and the grid. This paper aims to give an overview of the different factors influencing supraharmonic emissions from electric vehicles and studies the propagation of supraharmonic currents through a small, low-voltage grid. Measurements in an unique lab representing a possible future household gave valuable insight on the possible developments in primary and secondary supraharmonic emissions in a conventional or power-electronic-dominated system. Emission is, for some vehicles, influenced by the type of grid connection, whereas others show no difference in emission. The supraharmonic currents mainly stay within the local installation due to absorption of nearby devices. The level of voltage distortion is dependent on the connection impedance. During the measurements, another type of interaction between devices is observed in the form of “frequency beating” and intermodulation, in some cases resulting in the tripping of residual current devices. This interaction is further analyzed in order to better understand the possible impact it can have on the grid.

Research on q-p-shaped elevated traffic system in wetland and forest parks

Ecological protection is the basis of the construction of wetland and forest parks and therefore any development and utilization should take it as the premise. The traffic system planning and positioning of wetland and forest parks should also follow this principle. The establishment of the q-p-shaped elevated traffic system equipped with ring elevated passage and local installation of ground and over-ground viewing platforms in whole park can achieve the diversion of commuter cars, bicycles and walking tourists which is conducive to solving the problems of patch fragmentation, human activities interference and single viewing form in wetland construction. In this paper, the ways of creating q-p-shaped elevated traffic system is introduced in detail and this study can provide reference for the planning and design of wetland and forest parks.

VADR: validation and annotation of virus sequence submissions to GenBank

BackgroundGenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to GenBank. Before this project, there was no analogous tool in use for non-influenza viral sequence submissions.ResultsWe developed a system called VADR (Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions. The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. The system identifies 43 types of “alerts” that (unlike the previous BLAST-based system) provide deterministic and rigorous feedback to researchers who submit sequences with unexpected characteristics. VADR has been integrated into GenBank’s submission processing pipeline allowing for viral submissions passing all tests to be accepted and annotated automatically, without the need for any human (GenBank indexer) intervention. Unlike the previous submission-checking system, VADR is freely available (https://github.com/nawrockie/vadr) for local installation and use. VADR has been used for Norovirus submissions since May 2018 and for Dengue virus submissions since January 2019. Other viruses with high numbers of submissions will be added incrementally.ConclusionVADR improves the speed with which non-flu virus submissions to GenBank can be checked and improves the content and quality of the GenBank annotations. The availability and portability of the software allow researchers to run the GenBank checks prior to submitting their viral sequences, and thereby gain confidence that their submissions will be accepted immediately without the need to correspond with GenBank staff. Reciprocally, the adoption of VADR frees GenBank staff to spend more time on services other than checking routine viral sequence submissions.

NERDD: a web portal providing access to in silico tools for drug discovery

Summary The New E-Resource for Drug Discovery (NERDD) is a quickly expanding web portal focused on the provision of peer-reviewed in silico tools for drug discovery. NERDD currently hosts tools for predicting the sites of metabolism (FAME) and metabolites (GLORY) of small organic molecules, for flagging compounds that are likely to interfere with biological assays (Hit Dexter), and for identifying natural products and natural product derivatives in large compound collections (NP-Scout). Several additional models and components are currently in development. Availability and implementation The NERDD web server is available at https://nerdd.zbh.uni-hamburg.de. Most tools are also available as software packages for local installation. Contact [email protected]

Doc2Hpo: a web application for efficient and accurate HPO concept curation

We present Doc2Hpo, an interactive web application that enables interactive and efficient phenotype concept curation from clinical text with automated concept normalization using the Human Phenotype Ontology (HPO). Users can edit the HPO concepts automatically extracted by Doc2Hpo in real time, and export the extracted HPO concepts into gene prioritization tools. Our evaluation showed that Doc2Hpo significantly reduced manual effort while achieving high accuracy in HPO concept curation. Doc2Hpo is freely available at https://impact2.dbmi.columbia.edu/doc2hpo/. The source code is available at https://github.com/stormliucong/doc2hpo for local installation for protected health data.

Semantics for data in agriculture: a community-based wish list.

The paper reports on activities carried within the Agrisemantics Working Group of the Research Data Alliance (RDA). The group investigated on what are the current problems research and practitioners experience in their work with semantic resources for agricultural data, and elaborated the list of requirements that are the object of this paper. The main findings include the need to broaden the usability of tools so as to make them useful and available to the variety of profiles usually involved in working with semantics resources; the need to online platform to lift users from the burden of local installation; and the need for services that can be integrated in workflows. We further analyze requirements concerning the tools and services and provide details about the process followed to gather evidence from the community.

Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services.

Database identifier mapping services are important to make database information interoperable. BridgeDb offers such a service. Available mapping for BridgeDb link 1. genes and gene products identifiers, 2. metabolite identifiers and InChI structure description, and 3. identifiers for biochemical reactions and interactions between multiple resources that use such IDs while the mappings are obtained from multiple sources. In this study we created BridgeDb mapping databases for selections of genes-to-variants (and variants-to-genes) based on the variants described in Ensembl. Moreover, we demonstrated the use of these mappings in different software tools like R, PathVisio, Cytoscape and a local installation using Docker. The variant mapping databases are now described on the BridgeDb website and are available from the BridgeDb mapping database repository and updated according to the regular BridgeDb mapping update schedule.

Web-based hybrid-dimensional Visualization and Exploration of Cytological Localization Scenarios

Summary The CELLmicrocosmos 4.2 PathwayIntegration (CmPI) is a tool which provides hybriddimensional visualization and analysis of intracellular protein and gene localizations in the context of a virtual 3D environment. This tool is developed based on Java/Java3D/JOGL and provides a standalone application compatible to all relevant operating systems. However, it requires Java and the local installation of the software. Here we present the prototype of an alternative web-based visualization approach, using Three.js and D3.js. In this way it is possible to visualize and explore CmPI-generated localization scenarios including networks mapped to 3D cell components by just providing a URL to a collaboration partner. This publication describes the integration of the different technologies - Three.js, D3.js and PHP - as well as an application case: a localization scenario of the citrate cycle. The CmPI web viewer is available at: http://CmPIweb.CELLmicrocosmos.org.