Published since June 20, 2012

Bio-Algorithms and Med-Systems

ISSN: 1896-530X

Editor-in-chief: Irena Roterman-Konieczna

About this journal

Please note: The journal Bio-Algorithms and Med-Systems will no longer be published by De Gruyter after the end of 2022, therefore no new submissions will be accepted with immediate effect.

Objective
The journal Bio-Algorithms and Med-Systems (BAMS), edited by the Jagiellonian University Medical College, provides a forum for the exchange of information in the interdisciplinary fields of computational methods applied in medicine, presenting new algorithms and databases that allows the progress in collaborations between medicine, informatics, physics, and biochemistry. Projects linking specialists representing these disciplines are welcome to be published in this Journal. Articles in BAMS are published in English.

Topics

Bioinformatics
Systems biology
Telemedicine
E-Learning in Medicine
Patient's electronic record
Image processing
Medical databases

Article formats
Research Articles, Editorials, Review Articles and Mini Reviews, Short Communications

Review Articles and Mini Reviews are normally published by invitation, but suggestions to the Editors are welcome. Please find information about the submission process on the Submit-tab

Your Benefits

We are pleased to inform that prof. Irena Roterman-Konieczna, the Editor-in-Chief is listed in the World’s Top 2% Scientists in 2020 by Stanford University. This is a magnificent recognition for prof. Roterman-Konieczna insight and perseverance that have led to discoveries in the field of bioinformatics. Hearty congratulations!

Editor's Choice free access articles selection list

Bio-Algorithms and Med-Systems is proud to announce a new feature, the Editor's Choice free access article. To download the featured article free of charge, please click the link below:

Vol. 17, issue 4, Unparalleled and revolutionary impact of PET imaging on research and day to day practice of medicine, by Abass Alavi, Thomas J. Werner, Ewa Ł. Stępień and Paweł Moskal

Vol. 17, issue 3, Brain–computer interface for electric wheelchair based on alpha waves of EEG signal, by Kacper Banach, Mateusz Małecki, Maciej Rosół and Anna Broniec

Vol. 17, issue 2, Computational studies of the mitochondrial carrier family SLC25. Present status and future perspectives, by Andrea Pasquadibisceglie and Fabio Polticelli

Vol. 17, issue 2, International Conference Cybernetic Modelling of Biological Systems MCSB 2021

Vol. 17, issue 1, Bio-algorithms for the modeling and simulations of cancer cells and the immune response, by Muhammad Idrees and Ayesha Sohail

Please, see also the list of the most frequently cited articles published in BAMS, according to Web of Science and SCOPUS databases.

Overview

Your benefits:

Scientific and applicable projects linking medical issues and computer science
Broad range of topics (from molecular level of biological problems to the telemedicine)
New algorithms and databases
Extensive interdisciplinary collaboration
High quality peer-review

History

It is a tradition in our Department of Bioinformatics and Telemedicine to organize conferences in the field of Computer Simulation of Biological Systems. These conferences have been organized since 1975 in five years cycle.
The closing panel during the conference organized in 2005 opened the discussion concerning difficulties in publishing papers representing interdisciplinary issues. Particularly, linking the computer science activities in the medical field appeared to be difficult due to expectations of journals. The medical journals expected pure medical problems to be discussed. The computer science journals expected articles on new numerical solutions. Therefore, the papers presenting new computer-based techniques potentially applicable in both, scientific medicine as well as practical medicine, were postponed.
The students group participating in the conference in 2005 expressed the inspired the foundation of a journal which is specially oriented on the interdisciplinary activity linking medicine (and generally life science) with computer-based techniques.
As the result of this discussion the journal Bio-Algorithms and Med-Systems was launched and the first issue was published. The participants of the conference were the authors of the first issue, and the papers were published in Polish. The discussion about the cover and layout begun. The name of journal combines “Bio-Algorithms” to cover the field of molecular, cellular, tissue, organs, whole body simulations, and “Med-Systems” to cover all practical medical fields, including image processing, hospital system development, e-learning in medicine, etc. The second issue was published in English, thus opening the journal to the international community.
Bio-Algorithms and Med-Systems was registered officially; the owner of the title is the Jagiellonian University – Medical College. The first volumes were published bi-annually.
Right from the beginning we also offered a platform to the small business because the linking of scientific solutions with small companies was of high importance at that time.
Two issues of the Journal are of high importance to us. One issue is entirely devoted to grid systems as platform for integrated activities in medicine, and international project with contributors from Italy, Romania, France and China. The second issue focused on E-learning techniques in medicine, a project supported by a European grant and coordinated by British scientists.
We were very happy to be invited by De Gruyter to publish the Journal in cooperation. The collaboration with De Gruyter publisher started in 2012.
In our editorial activity we have been significantly supported by Cyfronet - Academic Computer Center AGH Krakow.
Since 2015 Bio-Algorithms and Med-Systems has been indexed by DBLP (computer science bibliography) data base, which means that citations are counted.

Publication frequency
2005 - 2010 – biannual
Since 2011 - quarterly

Previous Titles

Bio-Algorithms and Med-Systems

Back Issues

https://bit.wl.cm.uj.edu.pl/en/archival-issues/

Abstracting and Indexing

Bio-Algorithms and Med-Systems is covered by the following services:

Baidu Scholar
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Cabells Journalytics
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CNKI Scholar (China National Knowledge Infrastructure)
CNPIEC - cnpLINKer
DBLP Computer Science Bibliography
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EBSCO (relevant databases)
EBSCO Discovery Service
EMBASE
Genamics JournalSeek
Google Scholar
Index Copernicus
Japan Science and Technology Agency (JST)
J-Gate
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JournalTOCs
KESLI-NDSL (Korean National Discovery for Science Leaders)
Meta
Microsoft Academic
MyScienceWork
Naver Academic
Naviga (Softweco)
Primo Central (ExLibris)
ProQuest (relevant databases)
Publons
PubsHub
QOAM (Quality Open Access Market)
ReadCube
Reaxys
SCImago (SJR)
SCOPUS
Semantic Scholar
Sherpa/RoMEO
Summon (ProQuest)
TDNet
Text Mining
Ulrich's Periodicals Directory/ulrichsweb
WanFang Data
Web of Science - Emerging Sources Citation Index
WorldCat (OCLC)
Yewno Discover

Supplementary Materials

Topics

External Links

Volume 18 Issue 1

March 2022

Publicly Available March 24, 2022

Frontmatter

Page range: i-ii

Download PDF

Research Article

Open Access November 24, 2021

Development and implementation of an online platform for curriculum mapping in medical education

Jaroslav Majerník, Andrea Kacmarikova, Martin Komenda, Andrzej A. Kononowicz, Anna Kocurek, Agata Stalmach-Przygoda, Łukasz Balcerzak, Inga Hege, Adrian Ciureanu

Page range: 1-11

More Download PDF

Abstract

Objectives Nowadays universities face ever-increasing demands on quality of education, which is crucial from perspective of future graduates. In face of the need of constant quality improvements of medical curricula, it is important to seek strategies for their efficient management. The general trend is to develop electronic support tools to streamline the curricular design, analysis and harmonization. Methods Based on the requirements we have identified by the needs analysis among curriculum designers, teachers and managers at five universities involved in the Building Curriculum Infrastructure in Medical Education (BCIME) project, and evidence published in literature on curriculum development, we have developed methodological guidelines on curriculum innovations and a software-based tools that help manage, map and analyse curricula in the medical and healthcare study fields. Results In this paper, we share our experiences with building and implementation of EDUportfolio, an online platform developed within our consortium and intended to facilitate harmonisation and optimisation of medical outcome-based curricula. Its functionalities and outputs were verified by pilot mapping of Anatomy curricula as taught at partner universities in five European countries. Conclusions The visualisation and the analysis of described curriculum data using natural language processing techniques revealed both the hidden relations between curriculum building blocks and a set of overlaps and gaps in curricula. In addition, we demonstrate both the usability of the platform in the context of the involved academic environments and the capability to map and compare curricula across different institutions and different countries.

Review

November 25, 2021

Book review “Process maturity of hospitals and the quality of medical services” by Beata Detyna

Ryszard Tadeusiewicz

Page range: 13-15

Research Articles

October 12, 2021

Image processing algorithms in the assessment of grain damage degree

Wojciech Maliga, Włodzimierz Dudziński, Magdalena Łabowska, Jerzy Detyna, Marcin Łopusiewicz, Henryk Bujak

Page range: 17-28

Abstract

Objectives The paper presents preliminary results on the assessment of algorithms used in image processing of the grain damage degree. The purpose of the work is developing a tool allowing to analyse sample cross-sections of rye germs. Methods The analysis of the grain cross-sections was carried out on the basis of a series their photos taken at equal time intervals at a set depth. The cross-sections will be used to create additional virtual cross-sections allowing to analyse the whole sample volume. The ultimate plan is to generate two cross-sections perpendicular to each other. Based on volumetric data read from the sample section, a three-dimensional model of an object will be generated. Results The analysis of model surface will allowed us to detect possible grain damage. The developed method of preparing the research material and the proprietary application allowed for the identification of internal defects in the biological material (cereal grains). Conclusions The presented methodology may be used in the agri-food industry in the future. However, much research remains to be done. These works should primarily aim at significantly reducing the time-consuming nature of individual stages, as well as improving the quality of the reconstructed image.

February 21, 2022

The bioinspired traffic sign classifier

Dominika Przewlocka-Rus, Tomasz Kryjak

Page range: 29-38

Abstract

Objectives In this paper the research on developing convolutional spiking neural networks for traffic signs classification is presented. Unlike classical ones, spiking networks reflect the behaviour of biological neurons much more closely, by taking into account the time dimension and event-based operation. Spiking networks running on dedicated neuromorphic platforms, such as Intel Loihi, can operate with greater energy efficiency, hence they are an interesting approach for embedded solutions. Methods For convolutional spiking neural networks' design and simulation, Nengo and NengoDL libraries for Python language were used. Numerous experiments using the Leaky-Integrate-and-Fire (LIF) neuron model were conducted. The training results, with different augmentation methods and number of time steps for input image presentation were compared. Results Finally, an accuracy of up to 97% on the test set was achieved, depending on the number of time steps the input was presented to the SNN. Conclusions The proposed experiments show that using simple convolutional spiking neural network, one can achieve accuracy comparable to the classical network with the same architecture and trained on the same dataset. At the same time, running on dedicated neuromorphic hardware, such solution should be characterized by low latency and low energy consumption.

March 17, 2022

islEHR, a model for electronic health records interoperability

Arwa Najjar, Belal Amro, Mário Macedo

Page range: 39-54

Abstract

Objectives Due to the diversity, volume, and distribution of ingested data, the majority of current healthcare entities operate independently, increasing the problem of data processing and interchange. The goal of this research is to design, implement, and evaluate an electronic health record (EHR) interoperability solution – prototype – among healthcare organizations, whether these organizations do not have systems that are prepared for data sharing, or organizations that have such systems. Methods We established an EHR interoperability prototype model named interoperability smart lane for electronic health record (islEHR), which comprises of three modules: 1) a data fetching APIs for external sharing of patients’ information from participant hospitals; 2) a data integration service, which is the heart of the islEHR that is responsible for extracting, standardizing, and normalizing EHRs data leveraging the fast healthcare interoperability resources (FHIR) and artificial intelligence techniques; 3) a RESTful API that represents the gateway sits between clients and the data integration services. Results The prototype of the islEHR was evaluated on a set of unstructured discharge reports. The performance achieved a total time of execution ranging from 0.04 to 84.49 s. While the accuracy reached an F-Score ranging from 1.0 to 0.89. Conclusions According to the results achieved, the islEHR prototype can be implemented among different heterogeneous systems regardless of their ability to share data. The prototype was built based on international standards and machine learning techniques that are adopted worldwide. Performance and correctness results showed that islEHR outperforms existing models in its diversity as well as correctness and performance.

Ahead of Print / Just Accepted

Ahead of Print / Just Accepted

Volume 18 (2022)

Issue 1

Volume 17 (2021)

Volume 16 (2020)

Volume 15 (2019)

Volume 14 (2018)

Volume 13 (2017)

Volume 12 (2016)

Volume 11 (2015)

Volume 10 (2014)

Volume 9 (2013)

Volume 8 (2012)

Cite Score	0.7
Index Copernicus Value	120.66
Journal Citation Indicator	0.12
SCImago Journal Rank	0.151
Source Normalized Impact per Paper	0.349

Submit

Submission
You can easily submit your manuscript online. Simply go to http://mc.manuscriptcentral.com/bams and you will be guided through the whole peer-reviewing and publishing process.

Additionally, the Template for Ethical and Legal Declarations needs to be customized by the submitting author on behalf of all others and uploaded as a separate doc-file at the time of the original submission. Instructions on how to make declarations can be found here.

As per De Gruyter policy, no author list changes are permitted after acceptance of an article. The De Gruyter production team is instructed to enforce this policy during the production/proofing process.

Your benefits of publishing with us

Rapid publication times
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Free color illustrations
Optional open access publication
Accepted papers will be published online first as DOI-citable, forward-linked articles for quickest possible visibility for the scientific community
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Submission process

Submission of your paper via our submission management tool following the Information for Authors (you will be guided through every step)
As a condition of submission, the Template for Ethical and Legal Declarations must be customized by the submitting author on behalf of all other and uploaded as a separate Word file. Instructions on how to make declarations can be found here.
Single-blind peer review process
A decision on your paper is aspired within 2-4 weeks
Accepted articles are published online ahead of print approx. 3–4 weeks after acceptance

Please note

Manuscripts must be written in clear and concise English
Before submitting your article please have a look at our Ethical Guidelines and our Copyright Transfer Agreement
Once your article is accepted you have the option to publish it open access
Our Repository Policy allows you to distribute 30 PDF copies of your published article to colleagues (the PDF has to include the information that it is an author's copy). Please also feel free to distribute the link to the online abstract
If you have any general questions please visit our FAQ page for authors

We look forward to receiving your manuscript!

Hybrid Open Access

In this journal, authors have the option to publish their article under an open access license. Open Access allows you as an author to retain copyright and share your findings with colleagues and interested parties worldwide without any restraints.
Please note that authors from institutions with which we have a transformative agreement can publish open access without paying an article processing charge (APC). More information on the eligible institutions and articles can be found under the "Funding and Support" tab here.

Editorial

Editor-in-Chief
Prof. Irena Roterman-Konieczna, Jagiellonian University – Medical College, Krakow, Poland

Editorial Board
Prof. Piotr Augustyniak, AGH - University of Science and Technology, Krakow, Poland
Dr. Adam S.Z. Belloum, Instituut voor Informatica – University of Amsterdam, Amsterdam, Netherlands
Dr. Michal Brylinski, Louisiana State University, Baton Rouge, LA, USA
Dr. Marian Bubak, Department of Computer Science and ACC Cyfronet, AGH University of Science and Technology - Krakow, Poland / Informatics Institute, Amsterdam University - Amsterdam, Netherlands
Dr. Jacques Chomilier, Protein Structure Prediction Group, Insititut de Mineralogie et Physique des Milieux Condenses, Universite Pierre et Marie Curie, Paris, France
Prof. Marc Ebner, Ernst Moritz Arndt Universität Greifswald, Institut für Mathematik und Informatik, Greifswald, Germany
Dr. Dragan Gamberger, Rudjer Boskovic Institute Division of Electronics Laboratory for Information Systems, Zagreb, Croatia
Dr. Inga Hege, Medical Education Unit, University of Munich, Munich, Germany
Dr. Sören Huwendiek, University Children's Hospital Heidelberg, Heidelberg, Germany
Dr. Wiktor Jurkowski, Norwich Medical School, University of East Anglia, Norwich, UK
Prof. Kalina Kawecka-Jaszcz, Department of Cardiology and Hypertension, Institute of Cardiology, Jagiellonian Uniwersity, Medical College, Krakow, Poland
Prof. Leszek Konieczny, Jagiellonian University – Medical College, Krakow, Poland
Dr. Valeria Krzhizhanovskaya, Computational Science University of Amsterdam, Amsterdam, Netherlands
Prof. Pawel Moskal, Faculty of Physics, Astronomy and Applied Computer, Science, Jagiellonian University, Krakow, Poland
Dr. Gabriele Pierantoni, Trinity College Dublin, Dublin, Ireland
Prof. Fabio Polticelli, Department of Biology University Roma Tre, Rome, Italy
Dr. Mikhail Posypkin, Federal Research Center Computer Science and Control of the Russian Academy of Sciences, Moscow, Russia
Dr. Thomas Röblitz, University Center for Information Technology, University of Oslo, Norway
Prof. Reinhard Schneider, University of Luxembourg, Luxembourg, Luxemburg
Dr. Jian Shen, Department of Computer Engineering, Chosun University, Gwangju, Republic of Korea
Prof. Stanislaw J. Skrzypek, AGH - University of Science and Technology, Krakow, Poland
Dr. Pawel Spolnik, Jagiellonian University – Medical College, Krakow, Poland
Prof. Katarzyna Stapor, Silesian University of Technology, Gliwice, Poland
Prof. Ewa Stepien, Faculty of Physics, Astronomy and Applied Computer, Science, Jagiellonian University, Krakow, Poland
Prof. Ryszard Tadeusiewicz, AGH - University of Science and Technology, Krakow, Poland
Prof. Andrzej Walczak, Military University of Technology, Warsaw, Poland
Dr. Grzegorz Marcin Wojcik, Faculty of Mathematics, Physics and Computer Science
Institute of Computer Science – Laboratory of Neuroinformatics, Maria Curie-Sklodowska University, Lublin, Poland
Prof. Nabil Zary, Department of Learning, Informatics, Management and Ethics (LIME), Karolinska Institutet Stockholm, Stockholm, Sweden

Technical editors
Piotr Walecki, Zdzislaw Wisniowski, Anna Zaremba-Smietanska, Jagiellonian University Medical College, Krakow, Poland

Scientific contact
Department of Bioinformatics and Telemedicine
Sw. Lazarza 16, 31-530 Krakow, Poland
Email: bams@cm-uj.krakow.pl

Publisher contact
Zofia Szafranska-Czajka
De Gruyter
Email: bams.editorial@degruyter.com

(Deutsch)

Online ISSN: 1896-530X
Type: Journal
Language: English
Publisher: De Gruyter
First published: June 20, 2012
Publication Frequency: 4 Issues per Year
Audience: students, researchers and professionals in the field of computer science activity in medicine (and generally life science), medical ICT specialists and managers, innovation departments in enterprises connected with medicine and computer science