The 1st International Workshop
on Web Applications for Life Sciences

Logo WALS

8th July, 2022 in Bari, Italy


In conjunction with the 22nd International Conference on Web Engineering (ICWE 2022) - 5-8th July

About

The recent advances in unraveling the secrets of human conditions and diseases have encouraged new paradigms for their diagnosis and treatment. In addition, the COVID-19 pandemic has attracted increasing attention toward the genetic mechanisms of viruses and infected hosts. The information related to these phenomena is increasing at unprecedented rates, directly impacting the design and development of data management pipelines and their applications. New ways of processing and exposing data and knowledge on the Web in healthcare and life sciences environments are thus strongly needed.

The WALS workshop aims at being an initial meeting forum for Web Engineering, Data Management, and Bioinformatics researchers working on life sciences problems, offering the opportunity to share, discuss and find new approaches to support Search, Knowledge Extraction, and Data Science on the Web, thereby achieving important results for healthcare, precision medicine, biology, genomics, and virology.

The workshop welcomes submissions of fresh investigations and demonstrations concerning conceptual, experimental, and applied studies of life sciences problems on the Web. Directions of particular interest include: 1) monitoring and adaptation of Web Engineering techniques for life sciences; 2) design and engineering of Web applications for resolving life sciences problems; 3) development of crowdsourcing and collaborative strategies for life sciences data curation, integration, and discovery.

Topics of interest

The workshop focuses on Web Engineering as a means for facing the challenges that emerge when designing and developing applications for life sciences, focused on several branches such as healthcare, precision medicine, molecular biology, genomics, and virology. The workshop is not restricted to particular research methods, and we will consider conceptual, empirical, and applied research (including practical demonstrations). The topics of interest include, but are not limited to:

The topics of interest include, but are not limited to:

  • Web applications modeling and engineering for genomics
  • Web applications for the management of electronic/digital health records (EHR)
  • Web user interfaces for genomics, virology, or molecular biology
  • Development of Web systems for Precision Medicine
  • Web services for exploration of life sciences databases and knowledge graphs
  • Biological knowledge extraction
  • Genomic big data analytics
  • Web crowdsourcing methods for life sciences data curation and annotation
  • Information visualization and exploratory analysis methods for biology
  • Data science applications to healthcare and biology on the Web
  • Semantic Web knowledge representation for genomics
  • Life sciences Semantic Web applications
  • Biomedical ontologies engineering
  • Interoperability of health information systems and databases on the Web
  • Web Engineering techniques for FAIRification of biological datasets
  • COVID-19 and SARS-CoV-2 tracking via Web applications

Accepted papers

This is the list of accepted papers for WALS 2022:

  • Marco Antonio Tangaro, Marica Antonacci, Pietro Mandreoli, Daniele Colombo, Nadina Foggetti, Giacinto Donvito, Graziano Pesole and Federico Zambelli. The Laniakea Dashboard and storage encryption components: a foundation for developing on-demand cloud services for Life Science information on submission
  • Alberto García, Ana León, Mireia Costa, Oscar Pastor, Daniel González-Ibea, Estela Pérez-Román, Carles Borredà, Javier Terol, Victoria Ibanez, Francisco R. Tadeo and Manuel Talón. CitrusGenome: A Bioinformatics Tool to Characterize, Visualize, and Explore Large Citrus Variant Datasets information on submission
  • Paolo Perlasca, Marco Frasca, Cheick Tidiane Ba, Jessica Gliozzo, Marco Notaro, Mario Pennacchioni, Giorgio Valentini and Marco Mesiti. Integration and Visual Analysis of Biomolecular Networks

Paper submission guidelines

We invite submissions of high quality papers describing original and unpublished results regarding any of the workshop’s topics of interest.

Accepted papers will be included in the post-workshop proceedings to appear in Springer's series. The authors must submit manuscripts using the Springer-Verlag LNCS style for Lecture Notes in Computer Science. For style files and details, see the page http://www.springer.de/comp/lncs/authors.html. The workshop will accept two types of contributions:

  • Full papers - maximum 12 pages including references
  • Short/demo papers - maximum 6 pages including references

Papers must be submitted as PDF files using EasyChair at https://easychair.org/conferences/?conf=wals2022.

To ensure high quality, all papers will be thoroughly peer reviewed by the Program Committee. Manuscripts not submitted in the LNCS style or having more than 12 pages will be automatically rejected. The papers need to be original and not submitted or accepted for publication in any other workshop, conference, or journal.

For each accepted paper, at least one author must attend the workshop and present the paper. Registration is subject to the terms and conditions of ICWE.

Contact: anna.bernasconi@polimi.it

Post-conference publication

The papers accepted to the workshop, will be published within a Springer CCIS series volume as per the usual tradition of the ICWE conference joint events (see last year's ICWE 2021 Workshops).
In addition, they will be invited to submit a revised and extended version for a post-conference supplement in the journal BMC Bioinformatics or a similar venue (e.g., BMC Medical Informatics and Decision Making), depending on the topic.

The authors of accepted papers interested in submitting an extended article to a BMC supplement will need to fill, sign, scan and submit the supplement submission letter of interest. This document is important for us so we can know how many extended articles we will receive.
The authors can read the BMC Bioinformatics guidelines here and the BMC Medical Informatics and Decision Making guidelines here. There are no page limits for the BMC journals. The articles can be submitted on the BMC Supplements website.
The submitted extended articles will go through two review phases. In the first phase, the organizers of the WALS 2022 workshop will serve as guest editors. Some additional colleagues might be involved as additional guest editors, in case of high number of submissions. At the end of the first review phase, the guest editors will recommend the submitted extended articles for acceptance or rejection, and transfer them to the BMC journals' editor-in-chiefs who will take care of the second review phase.
The BMC editor-in-chiefs can decide to confirm the guest editors' recommendations or to start a new review phase (with new reviewers invited, new reviews, new requests, etc). The BMC editor-in-chief will eventually make the final decision on the acceptance or rejection of each extended manuscript.
Please note that, even if the guest editors suggest the acceptance for a specific paper, the BMC editor-in-chief can still decide to reject it (this case is quite rare but it can still happen).

Important dates (AoE)

  • Paper submission: April 24th, 2022, May 5th, 2022 (EXTENDED!)
  • Notification: May 31st, 2022
  • Workshop day: July 8th
  • Camera-ready version and copyright form: Sept 9th, 2022

Registration

The registration for the workshop is open via the ICWE website. At least one of the authors for each accepted paper must have a "Regular Registration" and attend the conference for paper presentation.

Organizers

Anna Bernasconi
Department of Electronics, Information, and Bioengineering - Politecnico di Milano, Italy
anna.bernasconi@polimi.it

Anna Bernasconi obtained her PhD cum laude at Politecnico di Milano, within the “Data-driven Genomic Computing” ERC Awarded project (2016-2021), under the supervision of Professor Stefano Ceri. She is now a postdoctoral researcher in the Department of Electronics, Information, and Bioengineering also at Politecnico di Milano. Her research focuses on conceptual modeling, data integration, semantic web, and biological data analysis. Since the COVID-19 pandemic, her research has moved to viral genomics, by building models, databases, and Web search systems for viral sequences and their variants.



Giuseppe Agapito
Department of Law, Economics and Social Sciences - "Magna Græcia" University of Catanzaro, Italy.
agapito@unicz.it

Giuseppe Agapito is an assistant professor and a senior research scientist in the field of Parallel and Distributed Computing, Machine Learning, Omics and Biological Networks data Analysis at the University Magna Græcia, of Catanzaro, Italy. His research interests are focused on the study of machine learning methods that can be used to take advantage of the vast amount of data that are produced nowadays. In particular, the research focuses on the development, implementation, and application of computational intelligence techniques for addressing complex real-world problems in different domains, especially in the field of biology and omics sciences.



Luca Nanni
Department of Computational Biology (DBC) - University of Lausanne, Switzerland
luca.nanni@unil.ch

Luca Nanni works as a Postdoctoral fellow in the Computational Systems Oncology laboratory at University of Lausanne, led by Professor Giovanni Ciriello. He received his PhD cum laude in 2021 in Computer Science and Engineering at Politecnico di Milano, Italy, under the supervision of Professor Stefano Ceri. His work focuses on the modeling of DNA conformation in the three-dimensional space using statistical and algorithmic methodologies, with a specific interest in cancer and aneuploid genomes. His work lies at the intersection of computer science, bioinformatics, computational biology and statistics and big data management.



Pietro Pinoli
Department of Electronics, Information, and Bioengineering - Politecnico di Milano, Italy
pietro.pinoli@polimi.it

Pietro Pinoli works as Researcher Fellow and lecturer at the Department of Electronics, Information and Bioengineering at the Politecnico di Milano (Italy). He received his PhD cum laude in 2017, with a thesis titled “Modeling and Querying Genomic Data” where he proposed and benchmarked data structures and algorithms to manage, search and elaborate huge collections of genomic datasets, by means of cloud and distributed technologies. He has been visiting PhD candidate at Harvard University (Cambridge, MA, US). His research interests include bioinformatics and computational biology, data bases and data management, big data technology and algorithms, machine learning and natural language processing, and drug repurposing.

Program Committee

  • Arif Canakoglu, Policlinico di Milano Ospedale Maggiore - Fondazione IRCCS Ca' Granda
  • Mario Cannataro, Magna Graecia University
  • Stefano Ceri, Polytechnic University of Milan
  • Carlo D'Eramo, Technical University of Darmstadt
  • Jose Luis Garrido, University of Granada
  • Giancarlo Guizzardi, University of Twente
  • Ana León Palacio, Universitat Politècnica de València
  • Sergio Lifschitz, Pontifical Catholic University of Rio de Janeiro
  • Oscar Pastor, Universitat Politècnica de València
  • Rosario Michael Piro, Polytechnic University of Milan
  • José Fabián Reyes Román, Universitat Politècnica de València
  • Pasquale Stano, University of Salento
  • Emanuel Weitschek, Uninettuno University

Invited Talk

Raffaele A. Calogero (Dept. of Molecular Biotechnology and Health Sciences, University of Torino).

My research experience was devoted to the development and optimization of analysis workflows and in mining transcription-based experiments, mainly in the oncology framework. An important aspect of my past and present work was the constant focus on new technologies (e.g. today single-cell and single-molecule sequencing) and their integration in our analysis workflows.
I started my journey in Bioinformatics in latest 90’s when I developed a tool to simulate, for windows-based PCs, a molecular biology laboratory (Iazzetti, et al., 1998). In 1998, I established at University of Torino the Genomics and Bioinformatics unit (B&Gu). B&Gu is an interdisciplinary group devoted to the study of multifactorial diseases by mean of high throughput technologies - i.e. microarray, Next Generation Sequencing – and bioinformatics. Since then my interests moved to research topics in which computational approaches could be used to mine biological data. Those years were the period in which expression microarrays started to be an effective tool to investigate genes involved in diseases and general biological processes. I was involved in various studies in which microarray data analysis played an important role. In collaboration with the group of cancer immunologists leaded by Prof. Forni at University of Torino, I focused the work of my group on the identification ofnew targets for anti-tumor vaccination protocols Because of my experience in microarray data analysis, my group was involved in a large number of collaborations in Italy and abroad. It is notable that, using gene expression microarrays, we were able to identify for the first time the presence of coding transcripts in circulating blood vesicles (Bruno,et al., 2009; Deregibus, et al., 2007; Herrera, et al., 2010), today a very hot topic in the field of biomarker discovery.
More recently we move our interest to single-cell transcriptomics both focusing in tool development (Alessandrì et al. Gigascience 2019) and data analysis (Rodriguez-Fraticelli et al. Nature 2018).
Since I started my research career as molecular biologist, I am convinced that genomics/transcriptomics data analysis, at least to some extent, should be placed back in the hands of wet biologists, thus itis more than 20 years that I am involved in training of PhD and Post-docs int he transcriptomics field, running courses at University of Naples first, thenat University of Turin (Sponsored by Affimetrix first and later by lllumina), at EMBL-Heidelberg, DUKE-NUS in Singapore and Italian Institute of Technology in Genova. Thus, with my group I have developed tools to simplify data analysis for microarray first (Sanges, et al., 2007) and then for Next generation sequencing (Beccuti, et al., 2017; Beccuti, et al., 2018) and single-cell transcriptomics today (Alessandrì et al. 2019). I am also the cofounder of the Reproducible Bioinformatics Project (Kulkarni et al. 2018), a community of bioinformaticians aiming to the creation of easy to use and reproducible bioinformatics workflows (http://www.reproducible-bioinformatics.org/).

Topic: Are web applications fulfilling the needs of life science scientists?

Talk abstract: Since biology and medicine are disciplines generating a massive amount of complex and hard-to-decipher data, bioinformatics is pervading the life science fields. Consequently, bioinformatics is a constantly growing field, producing a massive amount of computing tools. However, life science suffers from the lack of an adequate number of bioinformaticians. Furthermore, the number of life scientists understanding the need of building a background in basic programming is still very limited. The critical points highlighted above, taken together with the limited access to computing resources for many life scientists, have favored the development of a lot of web-based bioinformatics applications.
In this presentation, I wish to focus on the state of the art of web applications for life science and discuss their strength and limits. Furthermore, I wish to propose the possibility to move to more advanced web applications, where users can interact with them in a more sophisticated way, but without the need of acquiring coding skills, e.g. using syntax-free programming or a no-code approach.

Program

WALS session is on Friday July 8th, 09:00-10:30 (CEST) and 11.00-12.30. See the ICWE conference general program here.

09:00-09:30
Welcome and introduction to the workshop

09.30-10:30
Raffaele A. Calogero (Keynote talk):
Are web applications fulfilling the needs of life science scientists?

10:30-11:00
BREAK

11:00-11:30
Alberto García, Ana León, Mireia Costa, Oscar Pastor, Daniel González-Ibea, Estela Pérez-Román, Carles Borredà, Javier Terol, Victoria Ibanez, Francisco R. Tadeo and Manuel Talón:
CitrusGenome: A Bioinformatics Tool to Characterize, Visualize, and Explore Large Citrus Variant Datasets.

11:30-12:00
Marco Antonio Tangaro, Marica Antonacci, Pietro Mandreoli, Daniele Colombo, Nadina Foggetti, Giacinto Donvito, Graziano Pesole and Federico Zambelli:
The Laniakea Dashboard and storage encryption components: a foundation for developing on-demand cloud services for Life Science.

12:00-12:30
Paolo Perlasca, Marco Frasca, Cheick Tidiane Ba, Jessica Gliozzo, Marco Notaro, Mario Pennacchioni, Giorgio Valentini and Marco Mesiti:
Integration and Visual Analysis of Biomolecular Networks.

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