Resolving complex research data management issues in biomedical laboratories: Qualitative study of an industry-academia collaboration.

Abstract:

:This paper describes a distributed collaborative effort between industry and academia to systematize data management in an academic biomedical laboratory. Heterogeneous and voluminous nature of research data created in biomedical laboratories make information management difficult and research unproductive. One such collaborative effort was evaluated over a period of four years using data collection methods including ethnographic observations, semi-structured interviews, web-based surveys, progress reports, conference call summaries, and face-to-face group discussions. Data were analyzed using qualitative methods of data analysis to (1) characterize specific problems faced by biomedical researchers with traditional information management practices, (2) identify intervention areas to introduce a new research information management system called Labmatrix, and finally to (3) evaluate and delineate important general collaboration (intervention) characteristics that can optimize outcomes of an implementation process in biomedical laboratories. Results emphasize the importance of end user perseverance, human-centric interoperability evaluation, and demonstration of return on investment of effort and time of laboratory members and industry personnel for success of implementation process. In addition, there is an intrinsic learning component associated with the implementation process of an information management system. Technology transfer experience in a complex environment such as the biomedical laboratory can be eased with use of information systems that support human and cognitive interoperability. Such informatics features can also contribute to successful collaboration and hopefully to scientific productivity.

authors

Myneni S,Patel VL,Bova GS,Wang J,Ackerman CF,Berlinicke CA,Chen SH,Lindvall M,Zack DJ

doi

10.1016/j.cmpb.2015.11.001

subject

Has Abstract

pub_date

2016-04-01 00:00:00

pages

160-70

eissn

0169-2607

issn

1872-7565

pii

S0169-2607(15)00294-1

journal_volume

126

pub_type

杂志文章
  • pymia: A Python package for data handling and evaluation in deep learning-based medical image analysis.

    abstract:BACKGROUND AND OBJECTIVE:Deep learning enables tremendous progress in medical image analysis. One driving force of this progress are open-source frameworks like TensorFlow and PyTorch. However, these frameworks rarely address issues specific to the domain of medical image analysis, such as 3-D data handling and distanc...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2020.105796

    authors: Jungo A,Scheidegger O,Reyes M,Balsiger F

    更新日期:2021-01-01 00:00:00

  • MUSE--a new tool for interactive image analysis and segmentation based on multivariate statistics.

    abstract::MUSE--a new software tool for the interactive exploration of multivariate images and the development of image segmentation methods has been designed, implemented, and tested in a number of real application projects. The multivariate statistical classification and projection methods in MUSE can be used not only to anal...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/0169-2607(94)90128-7

    authors: Bengtsson E,Nordin B,Pedersen F

    更新日期:1994-03-01 00:00:00

  • Analysis of parameters affecting blood oxygen saturation and modeling of fuzzy logic system for inspired oxygen prediction.

    abstract:BACKGROUND AND OBJECTIVE:Fraction of Inspired Oxygen is one of the arbitrary set ventilator parameters which has critical influence on the concentration of blood oxygen. Normally mechanical ventilators providing respiratory assistance are tuned manually to supply required inspired oxygen to keep the oxygen saturation a...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2019.04.014

    authors: Radhakrishnan S,Nair SG,Isaac J

    更新日期:2019-07-01 00:00:00

  • predicting and improving the probability of live birth for women undergoing frozen-thawed embryo transfer: a data-driven estimation and simulation model.

    abstract:BACKGROUND AND OBJECTIVE:Frozen-thawed embryo transfer (FET) is now widely used for the treatment of infertility. For many couples and clinicians, concerns over the probability and how to increase the chance of a successful birth are very common. Currently, there is not a single model to predict the live birth outcomes...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2020.105780

    authors: Liang R,An J,Zheng Y,Li J,Wang Y,Jia Y,Zhang J,Lu Q

    更新日期:2021-01-01 00:00:00

  • A novel approach to speckle noise filtering based on Artificial Bee Colony algorithm: an ultrasound image application.

    abstract::In this study a novel approach based on 2D FIR filters is presented for denoising digital images. In this approach the filter coefficients of 2D FIR filters were optimized using the Artificial Bee Colony (ABC) algorithm. To obtain the best filter design, the filter coefficients were tested with different numbers (3×3,...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2013.05.009

    authors: Latifoğlu F

    更新日期:2013-09-01 00:00:00

  • Attitude of Iranian physicians and nurses toward a clinical decision support system for pulmonary embolism and deep vein thrombosis.

    abstract::This research project sought to design and implement a computerized clinical decision support system (CDSS) that was able to identify patients who were at risk of pulmonary embolism (PE) and deep vein thrombosis (DVT), as well as produce reminders for prophylactic action for these diseases. The main purpose of the CDS...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2014.03.007

    authors: Agharezaei Z,Bahaadinbeigy K,Tofighi S,Agharezaei L,Nemati A

    更新日期:2014-07-01 00:00:00

  • Detection of high-frequency respiratory movements during sleep.

    abstract::Sleep-related breathing disorders are common in adults and they have a significant impact on vigilance and quality of life. Previous studies have shown the validity of the static-charge-sensitive bed (SCSB) in monitoring breathing abnormalities during sleep. A whole nights sleep study produces a signal with considerab...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/s0169-2607(99)00043-7

    authors: Aittokallio T,Gyllenberg M,Järvi J,Nevalainen O,Polo O

    更新日期:2000-03-01 00:00:00

  • Predicting body fat percentage based on gender, age and BMI by using artificial neural networks.

    abstract::In the human body, the relation between fat and fat-free mass (muscles, bones etc.) is necessary for the diagnosis of obesity and prediction of its comorbidities. Numerous formulas, such as Deurenberg et al., Gallagher et al., Jackson and Pollock, Jackson et al. etc., are available to predict body fat percentage (BF%)...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2013.10.013

    authors: Kupusinac A,Stokić E,Doroslovački R

    更新日期:2014-02-01 00:00:00

  • A virtual environment to evaluate the arm volume for lymphedema affected patients.

    abstract:BACKGROUND AND OBJECTIVE:The paper presents a novel procedure based on 3D scanning and 3D modelling to automatically assess linear and volumetric measurements of an arm and to be further applied to patients affected by post breast cancer lymphedema. The aim is the creation of a virtual platform easily usable by medical...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2020.105795

    authors: Vitali A,Togni G,Regazzoni D,Rizzi C,Molinero G

    更新日期:2021-01-01 00:00:00

  • Epileptic EEG detection using neural networks and post-classification.

    abstract::Electroencephalogram (EEG) has established itself as an important means of identifying and analyzing epileptic seizure activity in humans. In most cases, identification of the epileptic EEG signal is done manually by skilled professionals, who are small in number. In this paper, we try to automate the detection proces...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2008.02.005

    authors: Patnaik LM,Manyam OK

    更新日期:2008-08-01 00:00:00

  • A program for the user-independent computation of the correlation dimension and the largest Lyapunov exponent of heart rate dynamics from small data sets.

    abstract::We propose a specially optimized computer program for the user-independent calculation of the correlation dimension D and the largest Lyapunov exponent L of heart rate dynamics on the basis of only 1024 electrocardiographically recorded RR intervals (heartbeat intervals). The validity of our program was established by...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 临床试验,杂志文章

    doi:10.1016/0169-2607(95)01707-0

    authors: Ganz RE,Lenz C

    更新日期:1996-01-01 00:00:00

  • An intelligent support system for automatic detection of cerebral vascular accidents from brain CT images.

    abstract:OBJECTIVE:This paper presents a Radial Basis Functions Neural Network (RBFNN) based detection system, for automatic identification of Cerebral Vascular Accidents (CVA) through analysis of Computed Tomographic (CT) images. METHODS:For the design of a neural network classifier, a Multi Objective Genetic Algorithm (MOGA)...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2017.05.005

    authors: Hajimani E,Ruano MG,Ruano AE

    更新日期:2017-07-01 00:00:00

  • A fast seed detection using local geometrical feature for automatic tracking of coronary arteries in CTA.

    abstract::We propose a fast seed detection for automatic tracking of coronary arteries in coronary computed tomographic angiography (CCTA). To detect vessel regions, Hessian-based filtering is combined with a new local geometric feature that is based on the similarity of the consecutive cross-sections perpendicular to the vesse...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2014.07.005

    authors: Han D,Doan NT,Shim H,Jeon B,Lee H,Hong Y,Chang HJ

    更新日期:2014-11-01 00:00:00

  • Analyzing hedyotis diffusa mechanisms of action from the genomics perspective.

    abstract:BACKGROUND AND OBJECTIVE:Hedyotis diffusa is an herb used for anti-cancer, anti-oxidant, anti-inflammatory, and anti-fibroblast treatment in the clinical practice of Traditional Chinese Medicine. However, its pharmacological mechanisms have not been fully established and there is a lack of modern scientific verificatio...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2018.10.019

    authors: Hu CJ,He J,Li GZ,Fang PP,Xie JD,Ding YW,Mao YQ,Hu KF

    更新日期:2019-06-01 00:00:00

  • IntroStat: a hypertext-based design for an electronic textbook to introduce biomedical statistics.

    abstract::A hypertext-based system called IntroStat has been developed to introduce fundamental methods of biomedical statistics. The system has been developed on a Macintosh II using HyperCard. It is written mainly in Hypertalk, a scripting language of HyperCard. Being an electronic textbook of probability and statistics, the ...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/0169-2607(95)01623-2

    authors: Okada M,O'Brien M

    更新日期:1995-04-01 00:00:00

  • Optimizations of the naïve-Bayes classifier for the prognosis of B-Chronic Lymphocytic Leukemia incorporating flow cytometry data.

    abstract::Prognosis of B-Chronic Lymphocytic Leukemia (B-CLL) remains a challenging problem in medical research and practice. While the parameters obtained by flow cytometry analysis form the basis of the diagnosis of the disease, the question whether these parameters offer additional prognostic information still remains open. ...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2012.02.009

    authors: Lakoumentas J,Drakos J,Karakantza M,Sakellaropoulos G,Megalooikonomou V,Nikiforidis G

    更新日期:2012-10-01 00:00:00

  • HEMET: mathematical model of biochemical pathways for simulation and prediction of HEpatocyte METabolism.

    abstract::Many computer studies and models have been developed in order to simulate cell biochemical pathways. The difficulty of integrating all the biochemical reactions that occur in a cell in a single model is the main reason for the poor results in the prediction and simulation of cell behaviour under different chemical and...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2008.06.004

    authors: De Maria C,Grassini D,Vozzi F,Vinci B,Landi A,Ahluwalia A,Vozzi G

    更新日期:2008-10-01 00:00:00

  • Evaluation of a smartphone-based assessment system in subjects with chronic ankle instability.

    abstract:BACKGROUND:Ankle sprain is the most common sports-related injury, and approximately 80% of patients studied suffered recurrent sprains. These repeated ankle injuries could cause chronic ankle instability, a decrease in sports performance, and a decrease in postural control ability. At the present time, smartphones have...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2016.11.005

    authors: Chiu YL,Tsai YJ,Lin CH,Hou YR,Sung WH

    更新日期:2017-02-01 00:00:00

  • Comparative analysis of active contour and convolutional neural network in rapid left-ventricle volume quantification using echocardiographic imaging.

    abstract::In cardiology, ultrasound is often used to diagnose heart disease associated with myocardial infarction. This study aims to develop robust segmentation techniques for segmenting the left ventricle (LV) in ultrasound images to check myocardium movement during heartbeat. The proposed technique utilizes machine learning ...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2020.105914

    authors: Zhu X,Wei Y,Lu Y,Zhao M,Yang K,Wu S,Zhang H,Wong KKL

    更新日期:2020-12-17 00:00:00

  • 3D shape analysis of the brain's third ventricle using a midplane encoded symmetric template model.

    abstract:BACKGROUND:Structural changes of the brain's third ventricle have been acknowledged as an indicative measure of the brain atrophy progression in neurodegenerative and endocrinal diseases. To investigate the ventricular enlargement in relation to the atrophy of the surrounding structures, shape analysis is a promising a...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2016.02.014

    authors: Kim J,Valdés Hernández Mdel C,Royle NA,Maniega SM,Aribisala BS,Gow AJ,Bastin ME,Deary IJ,Wardlaw JM,Park J

    更新日期:2016-06-01 00:00:00

  • Shape prior model via dual subspace segment projection learning.

    abstract:BACKGROUND AND OBJECTIVE:Shape prior models play a vital role for segmentation in medical image analysis. These models are most effective when shape variations can be captured by a parametric distribution, and sufficient training data is available. However, in the absence of these conditions, results are invariably muc...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2020.105760

    authors: Belous G,Busch A,Gao Y

    更新日期:2020-09-24 00:00:00

  • Utility of combining two diagnostic tests.

    abstract::Methods for evaluating a single diagnostic test with reference to the disease prevalence in a given population include sensitivity, specificity, positive predictive value, negative predictive value, and accuracy. Patient disease status and, ultimately, the treatment course is determined by the outcome of these diagnos...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/0169-2607(91)90119-e

    authors: Borowiak D,Reed JF 3rd

    更新日期:1991-07-01 00:00:00

  • Do false positive alerts in naïve clinical decision support system lead to false adoption by physicians? A randomized controlled trial.

    abstract:OBJECTIVES:False positive alerts in patient-safety-related clinical decision support systems (CDSS) are defined as alerts which incorrectly prompt when no-risk patients are encountered. It is an unfavorable condition which may potentially mislead physicians. The aim is to investigate physician responses toward false po...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章,随机对照试验

    doi:10.1016/j.cmpb.2016.04.011

    authors: Tsai CY,Wang SH,Hsu MH,Li YC

    更新日期:2016-08-01 00:00:00

  • Parameter identification and sedative sensitivity analysis of an agitation-sedation model.

    abstract::Sedation administration and agitation management are fundamental activities in any intensive care unit. A lack of objective measures of agitation and sedation, as well as poor understanding of the underlying dynamics, contribute to inefficient outcomes and expensive healthcare. Recent models of agitation-sedation dyna...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2006.06.011

    authors: Rudge AD,Chase JG,Shaw GM,Lee D,Hann CE

    更新日期:2006-09-01 00:00:00

  • An operator approach to interactive data processing. I. The system.

    abstract::A computer software system for interactive data processing is described. Data are transferred between functions ('operators'). Execution flow is designed in a semi-graphical language. Data are composed of arbitrary data types in sequences of any length. The system works as an interpreter and the user may define or mod...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/0169-2607(88)90025-9

    authors: Lööf Y

    更新日期:1988-09-01 00:00:00

  • An interactive medical image segmentation system based on the optimal management of regions of interest using topological medical knowledge.

    abstract::This paper presents an original interactive system for efficient medical image segmentation in computer aided diagnosis. The main originality concerns the method used to manage, according to an a priori topological-based structural model, regions of interest (ROIs) within which computations can be constrained. The goa...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2006.04.004

    authors: Fasquel JB,Agnus V,Moreau J,Soler L,Marescaux J

    更新日期:2006-06-01 00:00:00

  • Reliability and validity of DS-ADHD: A decision support system on attention deficit hyperactivity disorders.

    abstract:BACKGROUND AND OBJECTIVES:The purpose of this study is to examine the reliability of the clinical use of the self-built decision support system, diagnosis-supported attention deficit hyperactivity disorder (DS-ADHD), in an effort to develop the DS-ADHD system, by probing into the development of indicating patterns of p...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2016.12.003

    authors: Chu KC,Huang YS,Tseng CF,Huang HJ,Wang CH,Tai HY

    更新日期:2017-03-01 00:00:00

  • Coupling image processing and stress analysis for damage identification in a human premolar tooth.

    abstract::Non-carious cervical lesions are characterized by the loss of dental hard tissue at the cement-enamel junction (CEJ). Exceeding stresses are therefore generated in the cervical region of the tooth that cause disruption of the bonds between the hydroxyapatite crystals, leading to crack formation and eventual loss of en...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2010.06.009

    authors: Andreaus U,Colloca M,Iacoviello D

    更新日期:2011-08-01 00:00:00

  • Optic disc and optic cup segmentation based on anatomy guided cascade network.

    abstract:BACKGROUND AND OBJECTIVE:Glaucoma, a worldwide eye disease, may cause irreversible vision damage. If not treated properly at an early stage, glaucoma eventually deteriorates into blindness. Various glaucoma screening methods, e.g. Ultrasound Biomicroscopy (UBM), Optical Coherence Tomography (OCT), and Heidelberg Retina...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2020.105717

    authors: Bian X,Luo X,Wang C,Liu W,Lin X

    更新日期:2020-12-01 00:00:00

  • New Doppler-based imaging method in echocardiography with applications in blood/tissue segmentation.

    abstract::A parametric model for the ultrasound signals from blood and tissue is developed and a new imaging method, knowledge-based imaging, is defined. This method utilizes the likelihood ratio function to classify blood and tissue signals. The method separates blood and tissue signals by the difference in movement patterns i...

    journal_title:Computer methods and programs in biomedicine

    pub_type: 杂志文章

    doi:10.1016/j.cmpb.2009.03.012

    authors: Hovda S,Rue H,Olstad B

    更新日期:2009-10-01 00:00:00