On the development of MP-TOUGH2

The authors are developing MP-TOUGH2 for exploiting massively parallel computers. The goals of this effort are to (1) create a data-parallel subsurface transport code for solving larger problems than currently practical on workstations, (2) write portable code that can take advantage of scalability to run on machines with more processors, and (3) minimize the necessity for additional validation and verification of the resulting code. The initial strategy they have followed is to focus on optimizing the generic and time-consuming task of linear equation solution while leaving the bulk of TOUGH2 unmodified. In so doing, they have implemented a massively parallel direct solver (MPDS) that takes advantage of the banded structure of TOUGH2 Jacobian matrices. The authors have compared timings of the iterative conjugate gradient solvers DSLUBC, DSLUCS, and DSLUGM written in Fortran77 for the front end with the MPDS which uses the data parallel unit. The MPDS shows good performance relative to the iterative conjugate gradient solvers on the free-convection test problem. The robust direct solution provided by MPDS can be used to (1) check on the veracity of a given iterative conjugate gradient solution, or (2) be used on certain problems where iterative solvers fail to converge. The test problem used in this study is the Elder pure thermal convection problem. For generality, the authors use the TOUGH2 equation of state module EOS3 for water, air, and heat, although this particular problem is a single-phase flow problem

Mathematical modeling of permeation grouting and subsurface barrier performance

The injection of solution grouts into the subsurface can be used to form underground barriers for the containment of contaminants. The technology requires identifying suitable grout materials, specifically fluids which exhibit a large increase in viscosity after injection and eventually solidify after a controllable period, thus sealing permeable zones. The authors have developed a new fluid property module for the reservoir simulator TOUGH2 to model grout injection, taking into account the increase of liquid viscosity as a function of time and gel concentration. They have also incorporated into the simulator a model which calculates soil hydraulic properties after solidification of the gel within the pore space. The new fluid property module has been used to design and analyze laboratory experiments and field pilot tests in saturated and unsaturated formations under a variety of subsurface conditions. These applications include modeling barrier emplacement in highly heterogeneous soils in the vadose zone, grout injection into the saturated zone in combination with extraction wells for flow control, the design of verification strategies, and the analysis of barrier performance. In this paper the authors discuss the modeling approach and present simulation results of multiple grout injections into a heterogeneous, unsaturated formation

Basic Research Needs for Geosciences: Facilitating 21st Century Energy Systems

To identify research areas in geosciences, such as behavior of multiphase fluid-solid systems on a variety of scales, chemical migration processes in geologic media, characterization of geologic systems, and modeling and simulation of geologic systems, needed for improved energy systems

The UniProt-GO Annotation database in 2011

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set

Re-Annotation Is an Essential Step in Systems Biology Modeling of Functional Genomics Data

One motivation of systems biology research is to understand gene functions and interactions from functional genomics data such as that derived from microarrays. Up-to-date structural and functional annotations of genes are an essential foundation of systems biology modeling. We propose that the first essential step in any systems biology modeling of functional genomics data, especially for species with recently sequenced genomes, is gene structural and functional re-annotation. To demonstrate the impact of such re-annotation, we structurally and functionally re-annotated a microarray developed, and previously used, as a tool for disease research. We quantified the impact of this re-annotation on the array based on the total numbers of structural- and functional-annotations, the Gene Annotation Quality (GAQ) score, and canonical pathway coverage. We next quantified the impact of re-annotation on systems biology modeling using a previously published experiment that used this microarray. We show that re-annotation improves the quantity and quality of structural- and functional-annotations, allows a more comprehensive Gene Ontology based modeling, and improves pathway coverage for both the whole array and a differentially expressed mRNA subset. Our results also demonstrate that re-annotation can result in a different knowledge outcome derived from previous published research findings. We propose that, because of this, re-annotation should be considered to be an essential first step for deriving value from functional genomics data

Perspectives on tracking data reuse across biodata resources

c The Author(s) 2024. Published by Oxford University Press.Motivation: Data reuse is a common and vital practice in molecular biology and enables the knowledge gathered over recent decades to drive discovery and innovation in the life sciences. Much of this knowledge has been collated into molecular biology databases, such as UniProtKB, and these resources derive enormous value from sharing data among themselves. However, quantifying and documenting this kind of data reuse remains a challenge. Results: The article reports on a one-day virtual workshop hosted by the UniProt Consortium in March 2023, attended by representatives from biodata resources, experts in data management, and NIH program managers. Workshop discussions focused on strategies for tracking data reuse, best practices for reusing data, and the challenges associated with data reuse and tracking. Surveys and discussions showed that data reuse is widespread, but critical information for reproducibility is sometimes lacking. Challenges include costs of tracking data reuse, tensions between tracking data and open sharing, restrictive licenses, and difficulties in tracking commercial data use. Recommendations that emerged from the discussion include: development of standardized formats for documenting data reuse, education about the obstacles posed by restrictive licenses, and continued recognition by funding agencies that data management is a critical activity that requires dedicated resources

The human phylome

The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed

Current approaches to gene regulatory network modelling

Many different approaches have been developed to model and simulate gene regulatory networks. We proposed the following categories for gene regulatory network models: network parts lists, network topology models, network control logic models, and dynamic models. Here we will describe some examples for each of these categories. We will study the topology of gene regulatory networks in yeast in more detail, comparing a direct network derived from transcription factor binding data and an indirect network derived from genome-wide expression data in mutants. Regarding the network dynamics we briefly describe discrete and continuous approaches to network modelling, then describe a hybrid model called Finite State Linear Model and demonstrate that some simple network dynamics can be simulated in this model