ESB Webinar Series – No. 14 Why and how to do open and reproducible research
We announce with great pleasure the next webinar of the ESB Webinar Series about open and reproducible research.
Open and reproducible research movements have progressively gained attention across scientific disciplines. They aim to provide rigorous tools to support researchers in sharing data and code, collaborating with others, and contributing to greater field advancements. In this webinar, we will talk about (1) why we should work in an open and reproducible manner, and (2) how to make data, code, and publications open and reproducible. By the end of this webinar, you will learn:
– Why open and reproducible research favors rigor and collaboration in science
– How to share data openly
– How to create reproducible computational workflows
– How to include openness and reproducibility in publications
The webinar will be conducted by Serena Bonaretti (https://sbonaretti.github.io/). She is a senior scientist at Balgrist Campus (https://www.balgristcampus.ch/) in Zurich (Switzerland). Her main interests are musculoskeletal image acquisition and analysis combined with biomechanics, with applications to bone and joint diseases. In the last years, she has been dedicating time and efforts to do and promote open and reproducible research through community service (ORMIR community – https://ormircommunity.github.io/), talks, a YouTube channel (https://www.youtube.com/@serenabonaretti), and a free book entitled “Learn Python with Jupyter” (https://learnpythonwithjupyter.com/).
The seminar will last 45 minutes and will be followed by 15 minutes of Q/A from the audience. You will have the chance to ask your questions which will be addressed by the speaker at the end of the webinar. However, it would be great if you could send your question in advance while filling out the registration form or by sending it to email@example.com before the start of the webinar.
Click Here to register for the webinar.
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Looking forward to your attendance.
ESB Student Committee
ESB Webinar Series – No. 13 Modeling the glymphatic system using FEniCS
The discovery of the glymphatic system and meningeal lymphatics propose an alternative view on the basic metabolism of the brain. Perivascular spaces surround brain vessels and are now considered highways for the cerebrospinal fluid, allowing for entry of nutrients and clearance of neurotoxic solutes from the brain. This webinar discusses some recent findings and some of the recent models proposed for the system. In particular, we will discuss the role of sleep and some recently developed software tools for numerical simulations.
The webinar is conducted by Kent-Andre Mardal. Kent-Andre Mardal (born 1974) is a mathematician with a strong interest in biomedical applications and has for the last decade established an interdisciplinary collaboration on computational modeling of the physiology of the human brain, with researchers in both numerics, mechanics, and basic and clinical medicine, both nationally and internationally. He has been a core-developer of the internationally recognized software framework FEniCS, which has tens of thousands of users world-wide and the software is crucial in his biomedical application. Central in the application orient research is the development of core methodology for compatible, efficient discretization schemes.
ESB Webinar Series – No. 12 – TFMLAB: a user-friendly toolbox to calculate cell forces in 3D in vitro models
The mechanical forces that cells exert on the surrounding extracellular matrix are crucial for many physiological and pathological processes. Traction Force Microscopy is the most commonly used methodology to quantify cell forces in vitro. TFMLAB integrates all the computational steps to compute active cellular forces from confocal microscopy images, including image processing, cell segmentation, image alignment, matrix displacement measurement, and force recovery. Moreover, TFMLAB is accessible to non-technical users through interactive graphical user interfaces. At the end of the webinar, attendees will learn:
- The basics of computational TFM
- How to set-up TFMLAB
- The basic steps to run TFMLAB with a real example
- Visualizing TFMLAB results with Paraview
The webinar is conducted by Dr. Jorge Barrasa Fano. Jorge is a postdoctoral researcher at the Mechanobiology and Tissue Engineering group at KU Leuven. During his Ph.D., he focused on the development of computational methods to access mechanical information within 3D in vitro models of sprouting angiogenesis. The advanced in silico validation of these methods and the development of a user-friendly toolbox called TFMLAB were the main contributions of his Ph.D., which lead him to win the ESB Student Award in 2020. He recently obtained an FWO fellowship to carry out his postdoc research on the application of computational methods to in vitro experiments to investigate matrix remodeling and cell-ECM mechanics for disease.
ESB Webinar Series – No. 11 – Research Tools for: Collecting, Writing, Publishing and Disseminating your Research
This webinar provides an overview of the most important tools from searching the literature to disseminating the researcher’s outputs. The e-skills learned from the workshop are useful across various research disciplines and research institutions.
By the end of this webinar, attendees will learn how to:
- More efficiently use the tools that are available on the Net.
- Evaluate the types of literature that researchers will encounter.
- Convert the information of the search for a written document.
- Search and analyze the right journal to submit.
- Improve their publication’s visibility and impact
The webinar is conducted by Dr. Nader Ale Ebrahim who is well-known as the creator of “Research Tools” Box. Dr. Nader holds a PhD in Technology Management from the Faculty of Engineering, University of Malaya. Dr. Nader has collected over 700 tools that enable researchers to follow the correct path in research and ultimately produce high-quality research outputs with more accuracy and efficiency. Dr. Nader currently works as a “Research Visibility and Impact” freelancer consultant. Dr. Nader is also an adjunct lecturer at Alzahra University. He was working as a visiting research fellow with the Institute of Management and Research Services (IPPP), the University of Malaya from 2013 to November 2017. His current research interests are University rankings, Open access, Research visibility, Research Tools, and Bibliometrics. Dr. Nader provides assistance and guidance for researchers in disseminating and promoting their research work in order to enhance their research visibility and impact, as well as citations. He believes that the research cycle does not end with publications alone, thus he encourages pro-activeness in the dissemination of research outputs.
ESB Webinar Series – No. 10 – OpenFoam: a brief insight
This webinar aims to:
- Presenting a summary of OpenFOAM, including advantages and disadvantages in comparison to other softwares.
- Exploring the possibilities of OpenFOAM and reflecting on some publications that have used OpenFOAM from a biomechanical perspective.
By the end of the webinar, attendees will learn how to:
- Start using OpenFOAM
- Use its terminology
- Setup and run a test case
- Postprocess the results using Paraview
- Look at the library of resources
The webinar is conducted by Dr Sangita Swapnasrita. She is a postdoctoral researcher at MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University after finishing her PhD in 2021. She is a big fan of computational modelling and has worked with a range of software including MATLAB, LAMMPS (molecular dynamics), OpenFOAM (CFD) and COMSOL. Her PhD and Master’s thesis are both purely about computational modelling of physical processes. In her Master’s, she simulated the viscosity of lower alkanes and water using MATLAB and LAMMPS. And because that was so fun, she continued with modelling gas diffusion and reaction in porous structures using OpenFOAM for her PhD degree. Currently, she has migrated to modelling transport processes in the human kidney. She uses COMSOL and Python in conjugation to develop a mathematical microscope of the human kidney.
ESB Webinar Series – No. 9 – How Simpleware processes patient-specific anatomies in orthopedics
Simpleware provides a complete platform for analyzing 3D image data, integrating CAD-designs, and generating high-quality models for FE/CFD simulation. Simpleware benefits from an extensive range of tools to accurately process and analyze even the most complex structures. Offering options to customize and automate workflows, Simpleware is the ideal solution for life sciences, materials, and manufacturing applications.
The webinar will focus on the use of Synopsys Simpleware software in creating image-based models for orthopaedic applications. In particular we will be:
- Introducing Simpleware Software
- Reviewing the image to model workflow focusing on the segmentation of images to create 3D models
- Covering some of the application areas for these models once created.
The webinar is conducted by Dr. Ross Cotton. He is the ‘Applications Engineering Manager’ for the Simpleware software team at Synopsys, where he oversees the software technical support and consultancy projects. He has over 13 years’ experience working with academic, industry and hospital-based customers, providing solutions and support in image-based modelling workflows including simulation and 3D printing. Ross joined the Simpleware Software team in 2008 after receiving his PhD in Sports Engineering from Loughborough University (UK). The research combined experimental tests and numerical simulations to investigate the surface interactions of a soccer ball impact with the support of sports company Adidas.
ESB Webinar Series – No. 8 – Python – Everything you need for your daily scientific programming work
Python is a freely-available, easy-to-learn, open-source programming language with an incredible variety of free libraries. Currently, many scientific applications in our field like FE packages (e.g. Abaqus), visualization software (e.g. ParaView or VTK) or image processing tools (e.g. SimpleITK or 3D Slicer) use Python as scripting language.
This webinar aims to:
- Show how to get started
- Introduce to the main capabilities of Python, including numerical and scientific computing with Numpy/Scipy, plotting with Matplotlib, image processing with scikit-image, and Pandas data structures.
- Demonstrate a typical scientific application for data and image processing.
By the end of this tutorial, attendees will learn how to:
- Use core Python and Python libraries
- Get an idea about the possibilities with respect to your scientific programming work
We recommend that people who watch the webinar prepare the following:
- Install Anaconda Python (https://www.anaconda.com/products/individual)
- Explore Spyder IDE (comes with Anaconda) https://www.spyder-ide.org/ – watch the video on this page
- Read / try out the basic Python usage with Spyder
The webinar is conducted by Prof. Dr. Dieter Pahr, a full professor at TU-Wien and Karl Landsteiner University of Health Sciences in the field of biomechanics. He is giving an introductory lecture to mechanical engineering students at TU-Wien using Python. During his academic career, he developed the software medtool.
ESB Webinar Series – No.7 – Basics of agent-based computer modeling for clinically-related applications
This webinar is targeted towards individuals interested in agent-based computer modeling approaches to simulate biological processes. In particular, the webinar aims at:
- Introducing participants to the basics of agent-based modeling
- Providing examples of their application to investigate clinical-related problems.
By the end of the webinar, attendees will learn the basic principles to build an agent-based model including how to:
- Simulate individual agents
- Specify agent properties
- Define agent behavior and interactions
- Analyze and visualize model predictions
The webinar will be conducted by Prof. Sara Checa. She is a Junior Professor at the Julius Wolff Institute, Charite-Universitaetsmedizin Berlin, where she leads the research group of “Computational Mechanobiology”.
ESB Webinar Series – No.06 – CellProfiler: Making the most of your microscopy images with high-content image analysis
Microscopy images are coming to be recognized as the rich and quantitative data source that they have been since the advent of the digital image; many excellent image analysis tools now exist to help researchers find objects of interest in their data and extract measurements of images and/or objects.
In this webinar you will learn about:
- Using CellProfiler and/or other open-source tools to reproducibly identify objects and perform meaningful measurements.
- How to perform supervised classification and machine learning using CellProfiler Analyst.
- Identify connections between drugs, genes, and/or patient samples via morphological profiling using unsupervised classifications.
The webinar will be conducted by Dr. Beth Cimini who is the Lead Image Assay Developer for the Imaging Platform at the Broad Institute in Cambridge, MA and a CZI Imaging Scientist.
ESB Webinar Series – No.05 – ITK-SNAP: Open-Source Software for Medical Image Segmentation
The objective of this webinar is to introduce ITK-SNAP and provide an overview of its capabilities for medical image navigation and segmentation. In this webinar, attendees will learn some of the core capabilities of ITK-SNAP:
- Visualization of 3D medical image data
- Labeling of anatomical structures in 3D images both manually and semi-automatically
- Loading, editing, and saving segmentation files
- Rotating and landmarking 3D images
- Using the ITK-SNAP distributed segmentation service
The webinar will be Led by Dr. Paul Yushkevich (creator of ITK-SNAP) and by Dr. Alison Pouch from the Penn Image Computing and Science
ESB Webinar Series – No.04 – FEBio
FEBio is a freely-available finite element solver designed specifically for solving problems in computational biomechanics and biophysics. This webinar on the FEBio software project is focused mostly on new FEBio users and aims to:
- Introduce FEBio and provide an overview of its capabilities.
- Introduce FEBio Studio, a new integrated environment for setting up, running, and analyzing FEBio models.
ESB Webinar Series – No.03 (Co-organised with the student committee of the VPHi) -High-throughput Multicellular Simulation Studies with PHYSICELL by Prof Paul Macklin
Watch it at the VPHi website:
This webinar of the VPHi Keynote Webinar Series took place on 24 January 2020 at 16 CET featuring Prof Paul Macklin from Indiana University, under the moderation of Ngoc Mai Monica Huynh, member of the VPHi Student Committee. The webinar is endorsed and co-organised by the European Society of Biomechanics.
ESB Webinar Series – No.02 -Jumping into Musculoskeletal Modeling with OpenSim by Jennifer Hicks
This webinar is targeted toward individuals interested in learning how OpenSim can be used to explore topics in musculoskeletal simulation. The webinar is conducted by Dr. Jennifer Hicks, the Research and Development Manager of the OpenSim software project.
ESB Webinar Series – No.01 – Learn How to use SimVascular by Gabriel Maher
The video above explores SimVascular, an open source software package to simulate and analyze the cardiovascular system. SimVascular is the only fully open source software package providing a complete pipeline from medical image data segmentation to patient specific blood flow simulation and analysis.