LinkExplorer: Predicting, explaining and exploring links in large biomedical knowledge graphs

Machine learning algorithms for link prediction can be valuable tools for hypothesis generation. However, many current algorithms are black boxes or lack good user interfaces that could facilitate insight into why predictions are made. We present LinkExplorer, a software suite for predicting, explaining and exploring links in large biomedical knowledge graphs. LinkExplorer integrates our novel, rule-based link prediction engine SAFRAN, which was recently shown to outcompete other explainable algorithms and established black box algorithms. Here, we demonstrate highly competitive evaluation results of our algorithm on multiple large biomedical knowledge graphs, and release a web interface that allows for interactive and intuitive exploration of predicted links and their explanations.

AMAW: automated gene annotation for non-model eukaryotic genomes

SummaryTo support small and large-scale genome annotation projects, we present AMAW (Automated MAKER2 Annotation Wrapper), a program devised to annotate non-model unicellular eukaryotic genomes by automating the acquisition of evidence data (transcripts and proteins) and facilitating the use of MAKER2, a widely adopted software suite for the annotation of eukaryotic genomes. Moreover, AMAW exists as a Singularity container recipe easy to deploy on a grid computer, thereby overcoming the tricky installation of MAKER2.AvailabilityAMAW is released both as a Singularity container recipe and a standalone Perl script (https://bitbucket.org/phylogeno/amaw/)[email protected] or [email protected] informationSupplementary data are available at Bioinformatics online.

The Use of Augmented Reality in Collaboration Within the Construction Industry

Site visitation is a crucial aspect of civil engineers’ job scope as it provides them with first-hand construction data. However, due to the recent COVID-19 pandemic, construction site visitations are restricted, making the tasks of a civil engineer impossible to achieve. The main objective of this research is to find out and suggest a remedy to the problems commonly faced by civil engineers through the help of Augmented Reality (AR). Hence, the study’s objective is to analyse AR’s functionalities and suggest its best application to communicate spacious awareness via visual feedback for civil engineers. For maximum usability, an integrated software suite is proposed that provides access to AR worksites, measured data, and allows peer communication. This addressed the whole spectrum of problems faced by civil engineers with the switch to remote working. However, with the COVID-19 pandemic, the limitation of this project is that testing could not be executed to determine the efficacy of the said solution. Furthermore, the proposed solution has limitations, such as requiring pre-constructed infrastructure in applicable construction sites. Therefore, regular quality assurance (QA) and quality control (QC) are required to ensure proper functionality. In the future, AR LiDAR sensors could be a possibility as it provides increased accuracy of AR measurements which is critical in engineering.

Optimizing Bottom Hole Assembly Design Criteria to Improve Mechanical Performance in Slim Hole Drilling Environment

After analyzing the historical data of neighboring wells adjacent to the drilling site, 11 bit trips were required due to the low mechanical performance of the bottom hole assembly elements. This observation is based on maximum circulation hours and low helical bucking values that make it uneconomic to drill the sections with a positive displacement motor drive system. A redesign the bottom hole assembly was proposed to achieve an improved mechanical performance which allowed the section to be drilled with a single assembly. With a focus on increasing the mechanical limitations of the downhole elements, the use of 4 ¾" equipment is considered instead of the 3 ½" standard equipment used in this hole size. One of the biggest challenges was modifying the 4 ¾" positive displacement motor (PDM) to fit into the 5 ½" hole given that the mud motor has a maximum unmodified diameter of 5 ½". Using the force analysis module of a State-of-the-art BHA modelling software suite, multiple iterations were performed to simulate and validate an alternative PDM design and accompanying directional assembly. This new design featured modifications to an existing 4 ¾" PDM deploying a long gauge bit in combination with a fit for purpose measurement while drilling system. After numerous runs using this assembly design, it was found that there was no additional or unexpected wear of the modified Mud Motor components or associated elements of the downhole equipment. These observations act to validate the pre-job engineering force analysis. With the improved mechanical specifications of the 4 ¾" Bottom Hole Assembly (BHA) components, circulating hours were increased from 100 hours to 250+ hours in a stepwise process. This enabled drilling of the entire 5 ½" section with a single BHA, comparing favorably to the legacy approach with an average of eleven bit runs. The modified 4 ¾" PDM coupled with long gauge bit technology enabled a reduction in the oriented to rotate drilling ratio and an associated increase in the overall rate of penetration (ROP). It can be concluded that the substitution of 4 ¾" drilling equipment for 3 ½" in the 5 ½" hole section, increased the drilling efficiency between 30-50% according to field data obtained in Ukraine. The modified 4 ¾" PDM combined with long gauge bit technology has the potential to improve 5 ½" hole drilling performance in other locations. Following a structured planning process using State-of-the-art BHA modelling software suite enabling the evaluation of the significant forces that act in the drilling assembly and so significantly reducing the risks associated with exceeding the original design limits of the assembly. By improving the mechanical performance of the drilling assembly in a 5 ½" hole, new territory for drilling engineers and design engineers is now available to increase the drilling performance in slim wellbores.

Self-Service-Portale für das IT-Service-Request-Management: Identifikation relevanter Use-Cases

ZusammenfassungUnternehmen sind im Rahmen ihrer Digitalisierungsvorhaben vermehrt auf der Suche nach einem ihrer IT-Service-Management(ITSM)-Software-Suite ergänzenden Self-Service-Portal. Damit sollen sich Mitarbeiter über die im Service-Katalog enthaltenen IT-Services informieren und eigenständig unterschiedliche Service-Request-Arten auslösen können. Die Self-Service-Portal-Auswahl und -Einführung stellen Unternehmen jedoch vielfach vor eine Herausforderung. Als Gründe gelten insbesondere die hohe Komplexität von ITSM-Software-Suiten, deren vielschichtige Verzahnung innerhalb der Unternehmensarchitektur und der große, intransparente Tool-Markt. Zudem weisen die erhältlichen Self-Service-Portale im Standard gegenwärtig mehrheitlich einen relativ niedrigen Reifegrad auf. Die Forschung befindet sich im Bereich der Self-Service-Portale im Allgemeinen und bezüglich deren notwendigem Funktionsumfang im Besonderen noch relativ am Anfang und trägt somit wenig zur Problemlösung bei. Vor diesem Hintergrund geht vorliegender Beitrag im Rahmen einer explorativen Einzelfallstudie innerhalb eines Großunternehmens der Frage nach, welche Use-Cases (Service-Request-Typen) ein Self-Service-Portal abbilden sollte. Zentrales Ergebnis ist ein aus 16 Use-Cases bestehender Katalog, der als Referenz gleichermaßen für anbietende und einführende Unternehmen dienen kann. Der Beitrag zeigt, dass Mitarbeiter vielfältige Anliegen haben, die weit über die Neubestellung und Kündigung von IT-Services hinausgehen. Diesem Umstand sollte ein Self-Service-Portal gerecht werden.

The ISOTILT software for discovering cooperative rigid-unit rotations in networks of interconnected rigid units

A user-friendly web-based software tool called `ISOTILT' is introduced for detecting cooperative rigid-unit modes (RUMs) in networks of interconnected rigid units (e.g. molecules, clusters or polyhedral units). This tool implements a recently described algorithm in which symmetry-mode patterns of pivot-atom rotation and displacement vectors are used to construct a linear system of equations whose null space consists entirely of RUMs. The symmetry modes are first separated into independent symmetry-mode blocks and the set of equations for each block is solved separately by singular value decomposition. ISOTILT is the newest member of the ISOTROPY Software Suite. Here, it is shown how to prepare structural and symmetry-mode information for use in ISOTILT, how to use each of ISOTILT's input fields and options, and how to use and interpret ISOTILT output.

GSTools v1.3: A toolbox for geostatistical modelling in Python

Geostatistics as a subfield of statistics accounts for the spatial correlations encountered in many applications of e.g. Earth Sciences. Valuable information can be extracted from these correlations, also helping to address the often encountered burden of data scarcity. Despite the value of additional data, the use of geostatistics still falls short of its potential. This problem is often connected to the lack of user-friendly software hampering the use and application of geostatistics. We therefore present GSTools, a Python-based software suite for solving a wide range of geostatistical problems. We chose Python due to its unique balance between usability, flexibility, and efficiency and due to its adoption in the scientific community. GSTools provides methods for generating random fields, it can perform kriging and variogram estimation and much more. We demonstrate its abilities by virtue of a series of example application detailing their use.

How to Assign AMBER Parameters to Desmond-generated System with viparr4 v1

This tutorial partially copies steps from How to Assign CHARMM Parameters to Desmond-generated System with viparr4 but differs in the parametrization steps. You can use the Schrödinger software suite to prepare systems for molecular dynamics simulations, however, only the OPLS _2005 and OPLS4 force fields can be automatically assigned. This tutorial will show you how to use Desmond with third-party force fields like AMBER, using the Viparr utility from D.E. Shaw Research. You will prepare a protein-ligand complex, generate custom AMBER parameters for the ligand, and use the Viparr utility to convert the generated AMBER parameters into a viparr-formatted template, that can be used for simulations. You can find the input files for this tutorial here:

36 Effect of Blending and Tuning Relationship Matrices in Single-step Genomic BLUP

Single-step GBLUP (ssGBLUP) relies on the combination of genomic (G) and pedigree relationships for all (A) and genotyped animals (A22). The procedure implemented in the BLUPF90 software suite first involves combining a small percentage of A22 into G (blending) to avoid singularity problems, then an adjustment to account for the fact the genetic base in G and A22 is different (tuning). However, blending before tuning may not reflect the actual difference between pedigree and genomic base because the blended matrix already contains a portion of A22. The objective of this study was to evaluate the impact of tuning before blending on predictivity, bias, and inflation of GEBV, indirect predictions (IP), and SNP effects from ssGBLUP using American Angus and US Holstein data. We used four different scenarios to obtain genomic predictions: BlendFirst_TunedG2, TuneFirst_TunedG2, BlendFirst_TunedG4, and TuneFirst_TunedG4. TunedG2 adjusts mean diagonals and off-diagonals of G to be similar to the ones in A22, whereas TunedG4 adjusts based on the fixation index. Over 6 million growth records were available for Angus and 5.9 million udder depth records for Holsteins. Genomic information was available on 51,478 Angus and 105,116 Holstein animals. Predictivity and reliability were obtained for 19,056 and 1,711 validation Angus and Holsteins, respectively. We observed the same predictivity and reliability for GEBV or IP in all four scenarios, ranging from 0.47 to 0.60 for Angus and was 0.67 for Holsteins. Slightly less bias was observed when tuning was done before blending. Correlation of SNP effects between scenarios was > 0.99. Refined tuning before blending had no impact on GEBV and marginally reduced the bias. This option will be implemented in the BLUPF90 software suite.