Merge pull request #153 from Brainhack-Donostia/BHD2025

Bhd2025

Author: marco7877

.DS_Store

@@ -1,17 +1,14 @@
 <!-- Portfolio Grid Section -->
-    <section id="portfolio" class="bg-light-gray">
-        <div class="container">
-            <div class="row">
-                <div class="col-lg-12 text-center">
-                    <h2 class="section-heading text-yellow">BHD2025 Talks</h2>
-				          <h2 class="white mb-3"> The list of selected talks will be available soon!</h2>
-				        </div>
-				      </div>
-				    </div>
-                </div>
-            </div>
-			
-         <!-- >   <div class="row">
+<!-- Portfolio Grid Section -->
+<section id="portfolio" class="bg-light-gray">
+  <div class="container">
+    <div class="row">
+      <div class="col-lg-12 text-center">
+        <h2 class="section-heading text-yellow">BHD2025 Talks</h2>
+        <h2 class="white mb-3">We're currently working on the list of selected talks!</h2>
+      </div>
+    </div>
+             <div class="row">
             {% for post in site.posts %}
                 <div class="col-md-4 col-sm-6 portfolio-item">
                     <a href="#portfolioModal{{ post.modal-id }}" class="portfolio-link" data-toggle="modal">
@@ -30,5 +27,4 @@ <h4>{{ post.title }}</h4>
             {% endfor %}
             </div>
         </div>
-			 -->
     </section>

_includes/portfolio_grid.html

@@ -0,0 +1,20 @@
+---
+title: ""
+subtitle: " <br /> @  "
+layout: default
+modal-id: 4
+date: 2024-11-19
+img: 
+thumbnail: 
+alt: image-alt
+project-date: November 2025
+
+category: 
+description: ""
+
+bio: ""
+
+---
+
+
+

_posts/.markdown

@@ -1,19 +1,21 @@
 ---
-title: Programming transparency - Introduction to GitHub
-subtitle: "Marco Flores-Coronado - PhD Student <br /> @ BCBL"
+title: "TREASURE: An institutional pilot project to reward early stage researchers for reproducible, reusable, and open research practices and outputs at the University of Coimbra"
+subtitle: "Inês A. T. Almeida, Junior researcher <br /> @ University of Coimbra "
 layout: default
-modal-id: 1
-date: 2023-11-25
-img: marco_flores.jpg
-thumbnail: marcoyellow.png
+modal-id: 4
+date: 2024-11-19
+img: ines_almeida.png
+thumbnail: ines_almeida_noback.png
 alt: image-alt
-project-date: November 2023
+project-date: November 2025
 
-category:
-description: "There is a strong will within the research community for open science. Git repositories have become a tool for democratizing analysis pipelines, scientific software, and resource sharing. Moreover, Git allows researchers and developers to have transparency in their research methodology, with the potential for collaboration and community building besides frontiers. During this event, we will talk about the relevance of open-sourcing code while aiming to teach Git essential tools alongside the GitHub platform. Attendees will learn the basic Git workflow, Git commands, branching, undoing changes, and forking. All these tools will be useful for beginners and more experienced people during the hands-on projects part of BrainHack Donostia 2024."
-
-bio: "Marco completed his bachelor studies in Hispanic Philology and Literature at the National Autonomous University of Mexico. There, he carried out his own research project funded by the Psychology School regarding reading abilities in children with Autism Spectrum Disorder and eyetracking. Afterwards, he completed an MSc in Computational Modeling and Scientific Calculus with a specialization in robotics at the Autonomous University of Morelos State (UAEM), Mexico. During this period, he developed a computer model that simulated Cortical connections between different brain areas, and that accounts for audiovisual integration during speech perception. Soon after, he won a Caixa INPhINIT doctoral grant to continue his studies with a PhD in Cognitive Neurosciences at the Basque Center on Cognition Brain and Language (BCBL) and the University of the Basque Country (UPV-EHU) within the Signal Processing in Neuroimaging research group, and the Speech and Bilingualism group. Currently, he is developing analysis methods to improve MRI signal quality during overt speech production experiments. This will hinder investigation in speech production with MRI. His research interest is language processing but he follows a multidisciplinary perspective including tools from robotics, signal engineering, cognitive sciences, and computer science."
+category: 
+description: "Masters’ and PhD candidates earn their degree by completing a thesis, which typically contains one or more research articles. Yet, along the research path, researchers may create other outputs (e.g., protocols, methods, data, code), use reproducible and transparent practices (e.g., evidence synthesis, reporting guidelines, use of unique identifiers) and engage academics and non-academics to develop, conduct and disseminate (e.g., public engagement) the research. Implementing and sharing these practices and outputs accelerates progress by facilitating reuse, reproducibility and replication. To change research practice and culture, however, we must recognize and reward researchers for sharing more than research articles. 
+In this implementation-focused opt-in pilot program, we aim to offer University of Coimbra Masters’ and PhD candidates a formal reward for implementing reproducible, reusable and open research practices in their thesis research. We are co-creating the reward criteria with a Local Advisory Board (graduate students, course coordinators, and supervisors), with advice from an expert External Board. 
+The criteria include: (a) list of practices (e.g., reporting of null results, author contributions statements) and outputs (e.g., reusable step-by-step protocols, materials) from which the students can select, (b) assessment criteria for each practice/output (focus on quality), and (c) number of practices/outputs that must be implemented. The criteria are designed to be adaptable to different disciplines and projects. 
+The program will open in mid-2025. We will monitor participation, selected practices and outputs, and disciplines, for program improvement. In this talk we will present the program and share lessons learned during its development and implementation."
 
+bio: ""
 
 ---
 ---

_posts/2023-11-25-project-1.markdown

@@ -0,0 +1,40 @@
+---
+title: "When defaults return gibberish. Exploring different approaches to fitting models
+with categorical predictors (in R)"
+subtitle: "Inigo Urrestarazu - PreDoctoral Researcher \ <br /> @ Universidad del Pais Vasco "
+layout: default
+modal-id: 5
+date: 2024-11-19
+img: inigo_aziti.png
+thumbnail: inigo_aziti_noback.png
+alt: image-alt
+project-date: November 2025
+
+category: 
+description: "Statistical models frequently include categorical variables as predictors. By default, R
+handles these predictors using indicator coding: one level is treated as the reference
+(intercept), and the remaining levels are modeled as deviations from it. This convention
+often leads to outputs that are di@icult to interpret, particularly when the predictor has
+more than two levels. In such cases, model summaries only provide comparisons against
+the reference level, requiring additional pairwise comparisons to assess other contrasts.
+The complexity increases further with interaction terms, which also reflect deviations
+relative to the reference level. An alternative is sum coding, where levels are assigned
+equidistant numeric values that sum to zero. Although sum coding can be useful, it
+quickly becomes unintuitive when applied to variables with multiple levels. A third, more
+interpretable strategy is to index categorical predictors: the model estimates a
+conditional mean for each level, and contrasts of interest are computed post hoc. This
+approach simplifies interpretation. Besides, indexing categorical predictors aligns well
+with Bayesian regression, where priors must be placed on all model parameters, and
+assigning priors to conditional means is often conceptually and practically easier than
+assigning them to di@erences from a reference. This talk explores these three
+approaches—indicator coding, sum coding, and indexing—and discusses their
+implications for model interpretation and communication of results, both in Frequentist
+and Bayesian frameworks."
+
+bio: ""
+
+
+---
+
+
+

_posts/2023-11-25-project-2.markdown

@@ -1,26 +1,20 @@
 ---
-title: Standardizing Neuroimaging Data - Introduction to Brain Imaging Data Structure (BIDS)
-subtitle: "David Carcedo - Ryland Miller <br /> @ BCBL"
+title: "Coming soon"
+subtitle: "Nick Souter - Research Fellow \ <br /> @ University of Sussex "
 layout: default
-modal-id: 3
-date: 2023-11-26
-img: davidrywhite.png
-thumbnail: davidryyellow.png
+modal-id: 2
+date: 2024-11-19
+img: nick_souter.jpg
+thumbnail: nick_souter_noback.png
 alt: image-alt
-project-date: November 2023
-
-category: 
-description: "In the early 2000s, sharing neuroimaging data was a monumental task that was often not feasible. Each lab had their own way of organizing and naming the multitude of different possible files. The Brain Imaging Data Structure (BIDS) was introduced as an effort to correct this problem. By standardizing the format in which data is stored, it not only makes sharing data simple and easy, but also allows for software to be developed that will work on any data formatted according to BIDS. Thus, it is an important tool for any researcher in a modern world of open science and reproducibility. In this tutorial, Ryland and David will explain the basics of the BIDS format and then go into more in-depth examples of how to move datasets from their raw format into BIDS. David will talk about brain magnetic resonance imaging (MRI) data, whereas Ryland will talk about electroencephalography (EEG) data." 
-
-bio: "David holds a degree in Psychology from the University of the Basque Country (UPV). Additionally, he is a certified technician in diagnostic imaging and nuclear medicine (Inmakulada Tolosa). With 12 years of experience as a laboratory technician at the Basque Center on Cognition, Brain, and Language (BCBL), he serves as the MRI Coordinator at BCBL. During his master’s thesis (Universitat de Valencia), he worked extensively on converting a multimodal dataset from a BCBL project into BIDS format. This has involved magnetic resonance imaging (MRI) data, electroencephalography (EEG) data, neuropsychological questionnaires, and medical information collected over multiple time points and across three different treatment groups. Ryland received his Bachelor's degree in Computer and Information Sciences from the University of Oregon in 2018. He then worked as a Senior Research Technician in the Dosenbach and Greene Labs at Washington University in St. Louis School of Medicine. At WUSM, Ryland helped develop FIRMM (a software that tracks motion in real-time during functional MRI scans), maintained and improved scripts to analyze resting state functional MRI data, and taught programming skills to other lab members. He is currently completing his Master’s degree in the Cognitive Neuroscience of Language and working as a research assistant at the BCBL.  His main focus is on the proper and efficient use of computing resources in fMRI data analysis. To this end, he works on improving methodologies for MRI data collection, storage, and analysis and on teaching other researchers about these best practices."
-
----
-
-
+project-date: November 2025
 
+category:
+description: "The abstract of Nick's talk will be uploaded soon!"
 
 
 
+---