Abstract The problem of scheduling pre-operative assessment clinic (PAC) consists of assigning patients to a day for the exams needed before a surgical procedure, taking into account patients with different priority levels, due dates and operators availability. Realizing a satisfying schedule is of upmost importance for a hospital, since delay in PAC can cause delay in the subsequent phases, thus lowering patients’ satisfaction. In this paper, we propose a two-phase solution to the PAC problem: in the first phase, patients are assigned to a day taking into account a default list of exams; then, in the second phase, having the actual list of exams needed by each patient, we use the results of the first phase to assign a starting time to each exam. We first present a mathematical formulation for both problems. Further, we present a solution where modeling and solving are done via answer set programming. We then introduce a rescheduling solution that may come into play when the scheduling solution cannot be applied fully. Experiments employing synthetic benchmarks on both scheduling and rescheduling show that both solutions provide satisfying results in short time. We finally show the implementation and usage of a web application that allows to run our scheduling solution and analyze the results graphically in a transparent way.

Abstract A core part of the rehabilitation scheduling process consists of planning rehabilitation physiotherapy sessions for patients, by assigning proper operators to them in a certain time slot of a given day, taking into account several legal, medical, and ethical requirements and optimizations, for example, patient’s preferences and operator’s work balancing. Being able to efficiently solve such problem is of upmost importance, in particular after the COVID-19 pandemic that significantly increased rehabilitation’s needs. In this paper, we present a two-phase solution to rehabilitation scheduling based on Answer Set Programming, which proved to be an effective tool for solving practical scheduling problems. We first present a general encoding and then add domain-specific optimizations. Results of experiments performed on both synthetic and real benchmarks, the latter provided by ICS Maugeri, show the effectiveness of our solution as well as the impact of our domain-specific optimizations.

Abstract The rehabilitation scheduling process consists of planning rehabilitation physiotherapy sessions for patients, by assigning proper operators to them in a certain time slot of a given day, taking into account several requirements and optimizations, e.g. patient’s preferences and operator’s work balancing. Being able to efficiently solve such problem is of upmost importance, in particular as a consequence of the COVID-19 pandemic that significantly increased rehabilitation’s needs. The problem has been recently successfully solved via a two-phase solution based on answer set programming (ASP). In this paper, we focus on the problem of rescheduling the rehabilitation sessions, which comes into play when the original schedule cannot be implemented, for reasons that involve the unavailability of operators and/or the absence of patients. We provide rescheduling solutions based on ASP for both phases, considering different scenarios. Results of experiments performed on real benchmarks, provided by ICS Maugeri, show that also the rescheduling problem can be solved in a satisfactory way. Finally, we present a web application that supports the usage of our solution.

Abstract The Operating Room Scheduling (ORS) problem is the task of assigning patients to operating rooms (ORs), taking into account different specialties, lengths, and priority scores of each planned surgery, OR session durations, and the availability of beds for the entire length of stay (LOS) both in the Intensive Care Unit (ICU) and in the wards. A proper solution to the ORS problem is of primary importance for the healthcare service quality and the satisfaction of patients in hospital environments. In this paper we first present a solution to the problem based on Answer Set Programming (ASP). The solution is tested on benchmarks with realistic sizes and parameters, on three scenarios for the target length on 5-day scheduling, common in small–medium-sized hospitals, and results show that ASP is a suitable solving methodology for the ORS problem in such setting. Then, we also performed a scalability analysis on the schedule length up to 15 days, which still shows the suitability of our solution also on longer plan horizons. Moreover, we also present an ASP solution for the rescheduling problem, that is, when the offline schedule cannot be completed for some reason. Finally, we introduce a web framework for managing ORS problems via ASP that allows a user to insert the main parameters of the problem, solve a specific instance, and show results graphically in real time.

Abstract The problem of scheduling chemotherapy treatments in oncology clinics is a complex problem, given that the solution has to satisfy (as much as possible) several requirements such as the cyclic nature of chemotherapy treatment plans, maintaining a constant number of patients, and the availability of resources, for example, treatment time, nurses, and drugs. At the same time, realizing a satisfying schedule is of upmost importance for obtaining the best health outcomes. In this paper we first consider a specific instance of the problem which is employed in the San Martino Hospital in Genova, Italy, and present a solution to the problem based on Answer Set Programming (ASP). Then, we enrich the problem and the related ASP encoding considering further features often employed in other hospitals, desirable also in S. Martino, and/or considered in related papers. Results of an experimental analysis, conducted on the real data provided by the San Martino Hospital, show that ASP is an effective solving methodology also for this important scheduling problem.

The motivation of this work fits with the general vision to enable e-health for European citizens, irrespective of their social and financial status and their place of residence. Services to be provided include access to a high-quality early diagnostic and prognostic service for the Alzheimer Disease and other forms of dementia, based both on the European Research and Education Networks and the European Grid Infrastructure. The present paper reports on the architecture and services of a Science Gateway developed in the context of the DECIDE project, which aims to support the medical community in its daily duties of patients’ examination and diagnosis. The implementation of the Science Gateway is described with particular focus on the standard technologies adopted to ease the access by non IT-.expert users. The work leverages on an authentication and authorization infrastructure based on Identity Federations and robot certificates and on the adoption of the SAGA standard for middleware-independent Grid interaction. The architecture and the functionalities of the digital repository for medical image storage and analysis are also presented.

Abstract Scientific gateways in the form of web portals are becoming the popular approach to share knowledge and resources around a topic in a community of researchers. Unfortunately, the development of web portals is expensive and requires specialists skills. Commercial and more generic web portals have a much larger user base and can afford this kind of development. Here we present two solutions that address this problem in the area of portals for scientific computing; both take the same approach. The whole process of designing, delivering and maintaining a portal can be made more cost‐effective by generating a portal from a description rather than programming in the traditional sense. We show four successful use cases to show how this process works and the results it can deliver. Copyright © 2010 John Wiley & Sons, Ltd.

BACKGROUND: Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presents a novel method to perform correlations between microarray gene expression data and clinico-pathological data through a combination of available and newly developed processing tools. RESULTS: We developed Survival Online (available at http://ada.dist.unige.it:8080/enginframe/bioinf/bioinf.xml), a Web-based system that allows for the analysis of Affymetrix GeneChip microarrays by using a parallel version of dChip. The user is first enabled to select pre-loaded datasets or single samples thereof, as well as single genes or lists of genes. Expression values of selected genes are then correlated with sample annotation data by uni- or multi-variate Cox regression and survival analyses. The system was tested using publicly available breast cancer datasets and GO (Gene Ontology) derived gene lists or single genes for survival analyses. CONCLUSION: The system can be used by bio-medical researchers without specific computation skills to validate potential biomarkers or multi-gene classifiers. The design of the service, the parallelization of pre-processing tasks and the implementation on an HPC (High Performance Computing) environment make this system a useful tool for validation on several independent datasets.

BACKGROUND: Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientific impact and a wide application area. Several standalone applications had been developed in order to analyze microarray data. Two of the most known free analysis software packages are the R-based Bioconductor and dChip. The part of dChip software concerning the calculation and the analysis of gene expression has been modified to permit its execution on both cluster environments (supercomputers) and Grid infrastructures (distributed computing).This work is not aimed at replacing existing tools, but it provides researchers with a method to analyze large datasets without any hardware or software constraints. RESULTS: An application able to perform the computation and the analysis of gene expression on large datasets has been developed using algorithms provided by dChip. Different tests have been carried out in order to validate the results and to compare the performances obtained on different infrastructures. Validation tests have been performed using a small dataset related to the comparison of HUVEC (Human Umbilical Vein Endothelial Cells) and Fibroblasts, derived from same donors, treated with IFN-alpha.Moreover performance tests have been executed just to compare performances on different environments using a large dataset including about 1000 samples related to Breast Cancer patients. CONCLUSION: A Grid-enabled software application for the analysis of large Microarray datasets has been proposed. DChip software has been ported on Linux platform and modified, using appropriate parallelization strategies, to permit its execution on both cluster environments and Grid infrastructures. The added value provided by the use of Grid technologies is the possibility to exploit both computational and data Grid infrastructures to analyze large datasets of distributed data. The software has been validated and performances on cluster and Grid environments have been compared obtaining quite good scalability results.

Several systems have been presented in the last years in order to manage the complexity of large microarray experiments. Although good results have been achieved, most systems tend to lack in one or more fields. A Grid based approach may provide a shared, standardized and reliable solution for storage and analysis of biological data, in order to maximize the results of experimental efforts. A Grid framework has been therefore adopted due to the necessity of remotely accessing large amounts of distributed data as well as to scale computational performances for terabyte datasets. Two different biological studies have been planned in order to highlight the benefits that can emerge from our Grid based platform. The described environment relies on storage services and computational services provided by the gLite Grid middleware. The Grid environment is also able to exploit the added value of metadata in order to let users better classify and search experiments. A state-of-art Grid portal has been implemented in order to hide the complexity of framework from end users and to make them able to easily access available services and data. The functional architecture of the portal is described. As a first test of the system performances, a gene expression analysis has been performed on a dataset of Affymetrix GeneChip Rat Expression Array RAE230A, from the ArrayExpress database. The sequence of analysis includes three steps: (i) group opening and image set uploading, (ii) normalization, and (iii) model based gene expression (based on PM/MM difference model). Two different Linux versions (sequential and parallel) of the dChip software have been developed to implement the analysis and have been tested on a cluster. From results, it emerges that the parallelization of the analysis process and the execution of parallel jobs on distributed computational resources actually improve the performances. Moreover, the Grid environment have been tested both against the possibility of uploading and accessing distributed datasets through the Grid middleware and against its ability in managing the execution of jobs on distributed computational resources. Results from the Grid test will be discussed in a further paper.

BACKGROUND: The SYMBIOmatics Specific Support Action (SSA) is "an information gathering and dissemination activity" that seeks "to identify synergies between the bioinformatics and the medical informatics" domain to improve collaborative progress between both domains (ref. to http://www.symbiomatics.org). As part of the project experts in both research fields will be identified and approached through a survey. To provide input to the survey, the scientific literature was analysed to extract topics relevant to both medical informatics and bioinformatics. RESULTS: This paper presents results of a systematic analysis of the scientific literature from medical informatics research and bioinformatics research. In the analysis pairs of words (bigrams) from the leading bioinformatics and medical informatics journals have been used as indication of existing and emerging technologies and topics over the period 2000-2005 ("recent") and 1990-1990 ("past"). We identified emerging topics that were equally important to bioinformatics and medical informatics in recent years such as microarray experiments, ontologies, open source, text mining and support vector machines. Emerging topics that evolved only in bioinformatics were system biology, protein interaction networks and statistical methods for microarray analyses, whereas emerging topics in medical informatics were grid technology and tissue microarrays. CONCLUSION: We conclude that although both fields have their own specific domains of interest, they share common technological developments that tend to be initiated by new developments in biotechnology and computer science.