Suite Of Programs Research Articles

On extending and optimising the direct product decomposition

The concept of the direct product decomposition (DPD) is extended to arbitrary tensors while maintaining the same theoretical reduction in storage and computation. Additionally, the structure of the DPD as introduced by Gauss and Stanton is shown to be but one of a family of direct product decompositions which may be visualised using graphs. One particular member of this family is also shown to be critically important in relating the DPD and symmetry blocking approaches. Lastly, an implementation of tensor contraction using this extended DPD based on recent work in dense tensor contraction is presented, showing how the particular DPD used to represent the tensors in memory or on disk may be divorced from the optimal DPD used for a particular tensor contraction. The performance of the new algorithm is benchmarked by interfacing with the CFOUR programme suite, where significant speedups for CCSD calculations are observed.

Advancing consumer engagement: Supporting, developing and empowering youth leadership in cancer care.

Advancing consumer engagement: Supporting, developing and empowering youth leadership in cancer care.

On the Semidefinite Programming Algorithm for Energy-Based Acoustic Source Localization in Sensor Networks

The received energy has been becoming an efficient and attractive measure for acoustic source localization due to its cost saving in both energy and computation capability. We investigated the acoustic source localization problem based on received energy measurements in sensor networks. Focusing on the non-logarithmic energy attenuation model, we developed and compared a suite of semidefinite programming (SDP)-based source localization methods due to computational efficiency and numerical reliability. First, we proposed a general SDP-based estimator by jointly estimating the source location and the source radiation power. It yields an efficient estimate for both the scenario where the source is located inside the convex hull formed by sensors and the scenario where the source is located outside the convex hull. Next, a min–max approximation is given to cope with the applicable application of the existing energy-based source localization algorithms relying on the Gaussian energy noise assumption. Furthermore, a novel norm approximation method is proposed according to norm equivalence, which can provide a comparable performance with lower computational complexity. Simulations show that our proposed methods exhibit a superior performance than the existing energy-based source localization estimators.

High-temperature rotating cylinder rheometer for studying metallic glass forming liquids.

A high-temperature Couette rotating cylinder rheometer has been developed for shear viscosity investigations of metallic glass forming liquids under precisely controlled flow and environmental conditions. These materials generally exhibit viscosities in the range of 10-2 to 10-1 Pa s above their liquidus temperature. While knowledge of the viscosity is crucial for estimating the glass forming ability and processing capabilities of these liquids, accurate rheological measurements are challenging due to their vulnerability to oxidation and contamination from the crucible and processing environment. Thus, the present device was constructed to measure the shear viscosities of these reactive melts in an inert atmosphere using shear cells manufactured from isostatically pressed graphite. A custom suite of LabVIEW programs provides all the necessary data acquisition tools and controls for the motor, inductive generator, sample temperature, and torque sensor. The setup includes a proportional-integral-derivative controller that allows for both isothermal and continuous heating/cooling experiments from room temperature up to 1400 K. The system is calibrated using NIST reference oils at room temperature. To demonstrate the functionality of the apparatus at high temperatures, the viscosity of the metallic glass forming alloy Zr59.3Cu28.8Al10.4Nb1.5 (AMZ4) was measured above the melting point and was found to be in excellent agreement with previously reported reference values from levitation-based measurement techniques.

Structured lifestyle education for people with schizophrenia, schizoaffective disorder and first-episode psychosis (STEPWISE): randomised controlled trial.

Obesity is a major challenge for people with schizophrenia.AimsWe assessed whether STEPWISE, a theory-based, group structured lifestyle education programme could support weight reduction in people with schizophrenia. In this randomised controlled trial (study registration: ISRCTN19447796), we recruited adults with schizophrenia, schizoaffective disorder or first-episode psychosis from ten mental health organisations in England. Participants were randomly allocated to the STEPWISE intervention or treatment as usual. The 12-month intervention comprised four 2.5 h weekly group sessions, followed by 2-weekly maintenance contact and group sessions at 4, 7 and 10 months. The primary outcome was weight change after 12 months. Key secondary outcomes included diet, physical activity, biomedical measures and patient-related outcome measures. Cost-effectiveness was assessed and a mixed-methods process evaluation was included. Between 10 March 2015 and 31 March 2016, we recruited 414 people (intervention 208, usual care 206) with 341 (84.4%) participants completing the trial. At 12 months, weight reduction did not differ between groups (mean difference 0.0 kg, 95% CI -1.6 to 1.7, P = 0.963); physical activity, dietary intake and biochemical measures were unchanged. STEPWISE was well-received by participants and facilitators. The healthcare perspective incremental cost-effectiveness ratio was £246 921 per quality-adjusted life-year gained. Participants were successfully recruited and retained, indicating a strong interest in weight interventions; however, the STEPWISE intervention was neither clinically nor cost-effective. Further research is needed to determine how to manage overweight and obesity in people with schizophrenia.Declaration of interestR.I.G.H. received fees for lecturing, consultancy work and attendance at conferences from the following: Boehringer Ingelheim, Eli Lilly, Janssen, Lundbeck, Novo Nordisk, Novartis, Otsuka, Sanofi, Sunovion, Takeda, MSD. M.J.D. reports personal fees from Novo Nordisk, Sanofi-Aventis, Lilly, Merck Sharp & Dohme, Boehringer Ingelheim, AstraZeneca, Janssen, Servier, Mitsubishi Tanabe Pharma Corporation, Takeda Pharmaceuticals International Inc.; and, grants from Novo Nordisk, Sanofi-Aventis, Lilly, Boehringer Ingelheim, Janssen. K.K. has received fees for consultancy and speaker for Novartis, Novo Nordisk, Sanofi-Aventis, Lilly, Servier and Merck Sharp & Dohme. He has received grants in support of investigator and investigator-initiated trials from Novartis, Novo Nordisk, Sanofi-Aventis, Lilly, Pfizer, Boehringer Ingelheim and Merck Sharp & Dohme. K.K. has received funds for research, honoraria for speaking at meetings and has served on advisory boards for Lilly, Sanofi-Aventis, Merck Sharp & Dohme and Novo Nordisk. D.Sh. is expert advisor to the NICE Centre for guidelines; board member of the National Collaborating Centre for Mental Health (NCCMH); clinical advisor (paid consultancy basis) to National Clinical Audit of Psychosis (NCAP); views are personal and not those of NICE, NCCMH or NCAP. J.P. received personal fees for involvement in the study from a National Institute for Health Research (NIHR) grant. M.E.C. and Y.D. report grants from NIHR Health Technology Assessment, during the conduct of the study; and The Leicester Diabetes Centre, an organisation (employer) jointly hosted by an NHS Hospital Trust and the University of Leicester and who is holder (through the University of Leicester) of the copyright of the STEPWISE programme and of the DESMOND suite of programmes, training and intervention fidelity framework that were used in this study. S.R. has received honorarium from Lundbeck for lecturing. F.G. reports personal fees from Otsuka and Lundbeck, personal fees and non-financial support from Sunovion, outside the submitted work; and has a family member with professional links to Lilly and GSK, including shares. F.G. is in part funded by the National Institute for Health Research Collaboration for Leadership in Applied Health Research & Care Funding scheme, by the Maudsley Charity and by the Stanley Medical Research Institute and is supported by the by the Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London.

Extended measurements and an experimental accuracy effective Hamiltonian model for the 3ν2 and ν4+ν2 states of ammonia

The infrared spectrum of ammonia has proven to be highly problematic for effective Hamiltonian analysis. The most complete previous study of the 3ν2 and ν4+ν2 bands achieved the accuracy of 0.0069 cm−1 as reflected by the root-mean-square error of their fit, which is slightly more than 10 times the experimental accuracy. In the present study, we performed a global fit of the existing 2141 literature data involving 3ν2, ν4+ν2, 3ν2-ν2, (ν4+ν2)-ν2 together with 1281 new data involving 3ν2-2ν2, 3ν2-3ν2 and (ν4+ν2)-(ν4+ν2) using an effective Hamiltonian together with the Pickett suite of program SPFIT/SPCAT. The new dataset consists of three spectra recorded at the SOLEIL synchrotron facility. The effective Hamiltonian model proposed for 3ν2/ν4+ν2 has achieved experimental accuracy. This success combined with our previous success of the 2ν2/ν4 analysis leads us to believe that the vibrational states higher than 3ν2/ν2+ν4 may be analyzed with effective Hamiltonians as well.

Computational Tools in Forensic Anthropology: The Value of Open-Source Licensing as a Standard

Over the last 40 years, the number of computational tools in forensic anthropology has increased considerably. No longer are forensic anthropologists limited to the narrow suite of programs previously available, including Snow and Folk’s commingling probability calculator (1970), Maples’s more comprehensive “Forensic Anthropology” suite (1986), and Jantz and Ousley’s Fordisc (1993). Now at least 48 different tools have been independently developed, in part due to newly formulated programming languages and generally broader computer literacy of researchers in the field. While new tools enable a broader range of tasks to be addressed, many tools are closed source, some are not provided for community use, and others lack appropriate version control. Therefore, while the popularity of the microcomputer analytical tools is increasing, so too is their variation. Moreover, external validation of microcomputer test results lags behind development, because the source code is often not accessible to the larger community. Open-source licensing, as a standard, provides a path toward robust development, auditing, and validation of analytical tools; it encourages agile development, version control, and community-wide collaboration to facilitate reliability, which is favorable within the post-Daubert context. As a niche field with a relatively small user base that is subsequently unlikely to attract large commercial investment for thorough beta testing, open-source licensing thereby provides major benefits. This article focuses attention on these issues, advocates for open-source licensing of new and existing tools, and provides the first detailed review of microcomputer use in forensic anthropology since Maples’s first account in 1986 (some 32 years ago).

Swiftlink: a distributed, parallelised and scriptable linkage engine architecture for the 21st century

IntroductionMany currently extant generic tools for performing bulk linkage were developed last century and while they have accreted features to improve their utility they have failed to fully exploit modern computing architectures. Custom highly-parallelised and distributed solutions exist but there is a need for a modern generalised linkage toolkit.
 Objectives and ApproachThe aim of this project has been to design, from the ground up, a modern flexible, i.e. scriptable, linkage suite which also takes advantage of contemporary computing architectures to address issues such as distribution of computation, parallelisation of computation and cloud-based computation. Rather than being a monolithic linkage tool or a programming suite, a domain specific language has been developed to specifically describe linkage tasks. Linkage tasks written in this language are then 'executed' or 'compiled and run' to perform pair-wise calculations on data elements. Since linkage tasks are generally bespoke, scriptability has been an important consideration.
 ResultsDeveloping a domain specific linkage language has enabled problem specification to be more descriptive and flexible than a monolithic linkage application. The shift in focus from a programming language to a linkage language has enabled a corresponding shift in focus to linkage-related effort (such as blocking and comparison strategies) away from distracting 'glue' code which relates not to linkage tasks under consideration but rather to the distracting bookkeeping aspects of programme execution. The same linkage task may be compiled against different back ends and languages, e.g. FEBRL (python), swift, Amazon lambda (go). The architecture has enabled otherwise idle computing resource to be utilised as well as cloud-based computing facilities for increased throughput and performance. The architecture of the linkage system will be shown with examples.
 Conclusion/ImplicationsContemporary advances in computing sciences can and must be leveraged in modern linkage tools. By providing a custom scriptable linkage language, tasks may be more clearly specified in a manner more flexible than monolithic linkage applications and by uncoupling linkage specification from execution, linkage may be performed optimally across multiple machines and resources.

A DFT-based theoretical model for the calculation of spectral profiles of lanthanide M4,5-edge x-ray absorption.

This presentation reports the theoretical study of 3d core-electron excitation in lanthanide compounds in terms of electronic structure effects and optical properties. The calculations are done at the Density-Functional Theory (DFT) level complemented with an effective Hamiltonian based on ligand-field theory. The strategy consists of obtaining from DFT a totally symmetric density, where an active subspace is set up that forms the basis of the fivefold 3d and sevenfold 4f atomic orbitals of the lanthanide ion. This active subspace is defined with the fractional occupation of electrons, which represents open-shell species with the composite configuration 3d94fn+1. Based on the ligand-field analysis of the DFT results, the multiplet energies and ligand-field effects associated with the configuration 3d94fn+1 are evaluated; and the X-ray absorption spectra are simulated in terms of the intra-atomic 4fn → 3d94fn+1 electron transitions within the electric-dipole approximation. Examples for application are proposed taking into consideration the isolated trivalent lanthanides ions and compounds Cs2NaPrX6, with X = F, Cl, and Br. The results are compared with available experimental data, where a good agreement is qualitatively achieved. Also, the screening of the inter-electron repulsion and spin-orbit coupling interaction is numerically obtained that allows one to establish a fully non-empirical treatment of the 3d core-electron excitation, which can be valuable in the characterization and modeling of the spectral profiles of lanthanide M4,5-edge X-ray absorption spectroscopy. The enclosed theoretical model, which is being implemented in the Amsterdam Density Functional (ADF) suite of programs, is computationally economic and can be applied to any lanthanide system without limitations in terms of the size of the matrix elements of the effective Hamiltonian or the coordination symmetry of the lanthanide center.

An iterative approach to precondition inference using constrained Horn clauses

AbstractWe present a method for automatic inference of conditions on the initial states of a program that guarantee that the safety assertions in the program are not violated. Constrained Horn clauses (CHCs) are used to model the program and assertions in a uniform way, and we use standard abstract interpretations to derive an over-approximation of the set ofunsafeinitial states. The precondition then is the constraint corresponding to the complement of that set, under-approximating the set ofsafeinitial states. This idea of complementation is not new, but previous attempts to exploit it have suffered from the loss of precision. Here we develop an iterative specialisation algorithm to give more precise, and in some cases optimal safety conditions. The algorithm combines existing transformations, namely constraint specialisation, partial evaluation and a trace elimination transformation. The last two of these transformations perform polyvariant specialisation, leading to disjunctive constraints which improve precision. The algorithm is implemented and tested on a benchmark suite of programs from the literature in precondition inference and software verification competitions.

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens.

We have adapted the yeast 2-hybrid assay to simultaneously uncover dozens of transient and static protein interactions within a single screen utilizing high-throughput short-read DNA sequencing. The resulting sequence datasets can not only track what genes in a population that are enriched during selection for positive yeast 2-hybrid interactions, but also give detailed information about the relevant subdomains of proteins sufficient for interaction. Here, we describe a full suite of stand-alone software programs that allow non-experts to perform all the bioinformatics and statistical steps to process and analyze DNA sequence fastq files from a batch yeast 2-hybrid assay. The processing steps covered by these software include: 1) mapping and counting sequence reads corresponding to each candidate protein encoded within a yeast 2-hybrid prey library; 2) a statistical analysis program that evaluates the enrichment profiles; and 3) tools to examine the translational frame and position within the coding region of each enriched plasmid that encodes the interacting proteins of interest.

Synthesis and photophysical properties of blue-emitting fluorescence dyes derived from naphthalimide derivatives containing a diacetylene linkage group

Four naphthalimide-based dyes with a diacetylene linkage at the 3- or 4-position were synthesized to improve the thermal stability of the fluorescence dye as well as the efficiency of fluorescent emission at blue region. The absorption and fluorescence properties of the synthesized dyes were also investigated. The geometries and molecular orbitals of the dyes prepared were simulated using by density functional theory and time-dependent density functional theory using Gaussian 09. Furthermore, the suitability of the dyes for application in light-conversion films was examined. N-Phenyl groups were found to have a greater effect on the fluorescence of naphthalimide-based dyes than analogue containing an N-alkyl group. In addition, investigation of the effect of diacetylene linkages at the 3- or 4-positions of naphthalimide-based dyes showed that the fluorescence was influenced by the electron-donating effect of the diacetylene linkage which could afford more conjugation of π orbitals of the dyes. Four blue fluorescence dyes derived from 1,8-naphthalimide containing a diacetylene linkage were synthesized and then coated in PE film. The photophysical properties were analyzed using density functional theory (DFT) calculations, and excitations from the highest occupied molecular orbitals (HOMOs) to the lowest unoccupied molecular orbitals (LUMOs) of the dyes were simulated at the B3LYP/6-31G level of theory via the Gaussian 09 suite of programs. Using these methods, the influences of the position of the ethynyl linkages, alkyl groups, and phenyl groups on the electronic and fluorescence properties of the dyes were also clarified.

Polarized electron beams elastically scattered by atoms as a tool for testing fundamental predictions of quantum mechanics

Quantum information theory deals with quantum noise in order to protect physical quantum bits (qubits) from its effects. A single electron is an emblematic example of a qubit, and today it is possible to experimentally produce polarized ensembles of electrons. In this paper, the theory of the polarization of electron beams elastically scattered by atoms is briefly summarized. Then the POLARe program suite, a set of computer programs aimed at the calculation of the spin-polarization parameters of electron beams elastically interacting with atomic targets, is described. Selected results of the program concerning Ar, Kr, and Xe atoms are presented together with the comparison with experimental data about the Sherman function for low kinetic energy of the incident electrons (1.5eV–350eV). It is demonstrated that the quantum-relativistic theory of the polarization of electron beams elastically scattered by atoms is in good agreement with experimental data down to energies smaller than a few eV.

Recent advances in the UltraScan SOlution MOdeller(US-SOMO) hydrodynamic and small-angle scattering data analysis and simulation suite.

The UltraScan SOlution MOdeller (US-SOMO) is a comprehensive, public domain, open-source suite of computer programs centred on hydrodynamic modelling and small-angle scattering (SAS) data analysis and simulation. We describe here the advances that have been implemented since its last official release (#3087, 2017), which are available from release #3141 for Windows, Linux and Mac operating systems. A major effort has been the transition from the legacy Qt3 cross platform software development and user interface library to the modern Qt5 release. Apart from improved graphical support, this has allowed the direct implementation of the newest, almost two-orders of magnitude faster version of the ZENO hydrodynamic computation algorithm for all operating systems. Coupled with the SoMo-generated bead models with overlaps, ZENO provides the most accurate translational friction computations from atomic-level structures available (Rocco and Byron Eur Biophys J 44:417-431, 2015a), with computational times comparable with or faster than those of other methods. In addition, it has allowed us to introduce the direct representation of each atom in a structure as a (hydrated) bead, opening interesting new modelling possibilities. In the small-angle scattering (SAS) part of the suite, an indirect Fourier transform Bayesian algorithm has been implemented for the computation of the pairwise distance distribution function from SAS data. Finally, the SAS HPLC module, recently upgraded with improved baseline correction and Gaussian decomposition of not baseline-resolved peaks and with advanced statistical evaluation tools (Brookes et al. J Appl Cryst 49:1827-1841, 2016), now allows automatic top-peak frame selection and averaging.

Wellnet Integrated Care Program – supporting chronic disease management through private public partnerships

Introduction : Public and private funders have a mutual interest in effective chronic disease management at the primary care level due to its potential to reduce hospital admissions. The challenge lies in the complexity of the funding sources in Australia. The government’s Medicare system funds general practice on a fee for service basis, Primary Health Networks (PHNs) are government funded organisations commissioning care within local communities while private health insurers (PHIs) fund hospital care and are not permitted to insure GP services. Change implementation : Sonic Clinical Services (SCS), the primary care division of Sonic Healthcare, has implemented a model of chronic disease management that incorporates a pooled funding approach by private and public funders. SCS has partnered with PHNs and PHIs in a collaborative approach to resource primary care in a way that complements the Medicare fee for service structure. Aim of change : The WellNet Integrated Care Program is a suite of GP-led programs providing targeted and coordinated chronic disease management delivered through a Patient Centred Medical Home model which aims to shift the way patients are managed in primary care. The Medical Home approach shifts the epicentre of health care delivery from the clinician to the patient through a redesign of infrastructure, health care team roles and modes of delivering care. Developed by SCS, its unique elements include: Risk stratification according to level of risk and complexity Voluntary patient enrolments cdmNet, a web-based platform enabling care planning in real time across the entire clinical team Dedicated nurse care coordinator Change management support Stepped care approach Data analytics Target population : There are 5 programs targeting 4 population groups: FeelWell & GetWell - complex multi-morbidity BeWell - multiple morbidities StayWell - uncomplicated chronic disease LiveWell - at risk of chronic disease Highlights : SCS has partnered with Sydney North PHN and 4 PHIs to fund the BeWell program through 5 general practices in NSW. In Victoria, SCS has partnered with Australian Health Service Alliance, a service company representing a number of small to medium size PHIs, to deliver the program through 6 general practices. The start dates for these practices have been staggered with the earliest centre commencing enrolments in February 2017. The early results have included demonstrated improvement in care coordination, patient engagement and achievement of patient identified goals. Conclusion & discussion : The timeline for the program is 12 months with a formal independent evaluation undertaken at the conclusion of the pilot study. This funding model is sustainable as it is designed around the MBS funding system with affordable investment by PHNs and PHIs. The model is transferable to other partnerships who share the will to properly fund chronic disease management. Lessons : Lessons were learned around addressing different PHIs needs and expectations and finding consensus in the approach. Having a fully developed WellNet program with detailed workflows, costings and change management processes has proved to be the key to getting all the stakeholders on board.

Childhood Heart Disease - A partnership model of integrated care

HeartKids is a national charity supporting infants, children, young people and adults living with or impacted by congenital / childhood heart disease. For over 20 years HeartKids has worked in partnership with Lady Cilento Children's Hospital to deliver services and support to families.HeartKids supports families in hosptial and in the commuity with a suite of support programs lead by both health profesisonals and volunteers. Critical to our model of care is a partnership with Lady Cilento Children's Hospital which includes providing staff, resources and funding to families at the point of diagnosis and short and long term hosptial stays and bereavement support to families experiencing grief and loss.This presentation will describe the nature of the partnership, the collaborative arrangements in place between a non government agency and The Children's Health Service. The presentation will discuss from a famlies perspective the outcomes of the partnership including the impact and improvements on the health and well being of families during and post hospitalisation.The presentation will discuss the types of services used to engage families in particular the value of a case management approach delivered by HeartKids in collaboration with LCCH and the associated outcomes of each including parental confidence, reduced stress and anxiety. The presentation will also discuss the financial impact on families particularly regional and remote families and how HeartKids addresses this issue.The nature of the partnership will also be discussed including how communication flows between HeartKids and LCCH and how the two organisations' staff work collaboratively together. The challenges of working with families under stress will also be discussed and how HeartKids and LCCH social work team collaborate to reduce the impact of such.

SWRT: A package for semi-analytical solutions of surface wave propagation, including mode conversion, across transversely aligned vertical discontinuities

Abstract. We present a suite of programs that implement decades-old algorithms for computation of seismic surface wave reflection and transmission coefficients at a welded contact between two laterally homogeneous quarter-spaces. For Love as well as Rayleigh waves, the algorithms are shown to be capable of modelling multiple mode conversions at a lateral discontinuity, which was not shown in the original publications or in the subsequent literature. Only normal incidence at a lateral boundary is considered so there is no Love–Rayleigh coupling, but incidence of any mode and coupling to any (other) mode can be handled. The code is written in Python and makes use of SciPy's Simpson's rule integrator and NumPy's linear algebra solver for its core functionality. Transmission-side results from this code are found to be in good agreement with those from finite-difference simulations. In today's research environment of extensive computing power, the coded algorithms are arguably redundant but SWRT can be used as a valuable testing tool for the ever evolving numerical solvers of seismic wave propagation. SWRT is available via GitHub (https://github.com/arjundatta23/SWRT.git).

From Single Structures to Ensembles: Application of the Galaxy Program Suite to Ubiquitin, Cyclophilin a and PTP1B

From Single Structures to Ensembles: Application of the Galaxy Program Suite to Ubiquitin, Cyclophilin a and PTP1B

MetaQSAR: An Integrated Database Engine to Manage and Analyze Metabolic Data.

The study describes the MetaQSAR tool, a new database engine specifically tailored to collect and analyze metabolic data. This is a plug-in embedded in the VEGA suite of programs (freely downloadable at www.vegazz.net ) and takes advantage from all cheminformatics features implemented in the software with additional tools aimed to perform statistical analyses, similarity searches, and physicochemical profiling of the stored molecules. MetaQSAR also implements a novel metabolism classification, which groups the metabolic reactions in 101 classes and can find numerous applications in metabolic analyses. The potentials of MetaQSAR are here assessed by using it to store and analyze an extended database focused on metabolism of xenobiotics, which was collected by manually curated meta-analysis of the recent literature. The database includes 1890 substrates taken from about 1500 original papers in the years 2004-2015. The database was utilized in both physicochemical analyses and similarity searches, so evidencing the notable potentialities of MetaQSAR, which can find particularly fruitful applications in developing targeted predictive approaches.

Automated Voxel Placement: A Linux-based Suite of Tools for Accurate and Reliable Single Voxel Coregistration.

BackgroundSingle-voxel proton magnetic resonance spectroscopy (1H MRS) is a powerful technique for studying in vivo neurochemistry, but has an often-overlooked source of error variance: inconsistent voxel placement between scans. We developed and evaluated an Automated Voxel Placement (AVP) procedure for accurate and reliable 1H MRS voxel prescription. AVP is a suite of Linux-based programs that facilitate automated template-driven single-voxel coregistration.MethodsThree studies were conducted to evaluate AVP for prescription of one voxel: left dorsolateral prefrontal cortex. First, we evaluated how robust AVP was to ‘extreme’ subject head positions/angulations within the scanner head coil. Second, subjects (N = 13) were recruited and underwent MR scans. Manual voxel prescription (n = 5) was contrasted with AVP (n = 8). A subset of AVP subjects (n = 4) completed a second scan. Third, ongoing data collection (n = 16; recruited for a separate study) helped evaluate AVP. Voxel placement accuracy was quantified as 3D geometric voxel overlap percentage between each subject’s voxel and the template voxel. Reliability was quantified as 3D geometric voxel overlap percentage across subjects at each time point and within subjects who completed two scans.ResultsResults demonstrated that AVP was robust to ‘extreme’ head positions (97.5% - 97.9% overlap with the template voxel). AVP was significantly more accurate (baseline and follow-up: 96.2% ± 3.0% and 97.6% ± 1.4% overlap) than manual voxel placement (67.7% ± 22.8% overlap; ps<.05). AVP was reliable within- (97.9%) and between-subjects (94.2% and 97.2% overlap; baseline and follow-up; respectively). Finally, ongoing data collection indicates AVP is accurate (96.0%).ConclusionThese pilot studies demonstrated that AVP was feasible, accurate, and reliable method for automated single voxel coregistration.