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UU Research Engineering team
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Add projects to project list #1

Closed jelletreep closed 2 years ago

jelletreep commented 2 years ago

Create a list of projects. How should it look like? Plain list with links to project repositories? Short descriptions? Visuals?

jelletreep commented 2 years ago

Template:

| [project title](repo link) | 
| --- | 
| 10/2020-12/2020 |
| Faculty of ... ; Research groups |
| Technologies: ... | 
| RSEs: [rse name](uu or github profile page) |
| Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum |
qubixes commented 2 years ago 

| [ASReview](https://github.com/asreview/asreview) | 
| --- | 
| 2018-2021 |
| Faculty of Social Sciences |
| Machine learning, active learning, Python, flask, hyperparameter optimization, simulation | 
| Raoul Schram, Parisa Zahedi, Jonathan de Bruin |
| ASReview is a machine learning tool to aid researchers in performing systematic reviews. It uses active learning to present users with more likely relevant papers. It has been written in Python 3.7+, and hyper parameters have been optimized using the hyperopt package. We have also contributed to the initial back-end for the user interface using flask. | ```

| [Streetview 1](https://github.com/UtrechtUniversity/streetview-greenery) |
| --- | 
| 2019-2021 |
| Faculty of Geosciences |
| Machine learning, Python, image segmentation, deeplab, kriging, geolocation, CityScapes | 
| Raoul Schram |
| For the streetview project we have used the (formerly) open street view data from the municipality of Amsterdam to create a map of the greenness. This is done by taking the images and segmenting each image into different classes. The number of pixels in each image belonging to the "greenery" class is used to create the Amsterdam greenery map. | ```

| [Network Entropy](https://github.com/qubixes/temporal-network-synthesis) |
| --- | 
| 2020-2021 |
| Department of Information and Computing Sciences |
| Temporal networks, Python, numba, simulation | 
| Raoul Schram |
| To improve the theoretical analysis and comparison of different temporal networks, we have invented a new metric to study them. The measure is called network entropy, and is applicable to any temporal network. We showed with simulations that processes on a network behave very differently, depending on the network entropy. | ```

| [Protosc](https://github.com/UtrechtUniversity/protosc) |
| --- | 
| 2020-2021 |
| Faculty of Social Sciences |
| Feature selection, Python, image classification, wrapper, filter, genetic algorithm | 
| Raoul Schram, Roos Voorvaart |
| Protosc is a Python library that aims to determine which features are relevant to a given classification problem. It does so by using wrapper/filter/genetic algorithms, after which automatic statistical analysis is used to determine which features are significant. The package also includes a few different options for an image classification pipeline. | ```
qubixes commented 2 years ago

Btw, should we add former members to the RSE field? Could be confusing for people looking for contact to a specific RSE?

MartineDeVos commented 2 years ago

If a former member worked on a project, I think he/she should also be in the RSE field. Additionally, we could add a former members sublist to the "meet the team" section

RoelBrouwer commented 2 years ago

Another point of discussion for the recap (maybe): should the 'technologies' field be limited to technologies/expertise that we as research engineers developed/used, or should it rather be a list of keywords describing the project?

Also, do we refer to ourselves as RSEs, REs, Research Engineers, or anything else? Would be good to be consistent and clear about that :)

RoelBrouwer commented 2 years ago 
| [Ocean Parcels Numba](https://github.com/OceanParcels/parcels) | 
| --- | 
| 01/07/2021 - now |
| Faculty of Science |
| Technologies: Python, numba | 
| RSEs: [Roel Brouwer](uu.nl/staff/RJJBrouwer) and Raoul Schram |
| Investigating the feasibility of speeding up existing Python code for [Parcels](oceanparcels.org) using numba. The aim is to speed up the simulation enough to eliminate the need for a separate (partial) JIT/C path in the code. This should lead to a more flexible and maintainable code base. |

| [Ocean Parcels particle-particle interaction](https://github.com/OceanParcels/parcels) | 
| --- | 
| 01/07/2020 - 30/06/2021 |
| Faculty of Science |
| Technologies: Python, datastructures, simulation | 
| RSEs: [Roel Brouwer](uu.nl/staff/RJJBrouwer) and Raoul Schram |
| Providing a working implementation of particle-particle interaction for [Parcels](oceanparcels.org). The aim was to allow simulated particles to interact and influence each others states. This project involved reviewing and partially restructuring the data structures that Parcels uses for storing particle data, and implementing particle-particle interaction under certain conditions. |
MartineDeVos commented 2 years ago

If a former member worked on a project, I think he/she should also be in the RSE field. Additionally, we could add a former members sublist to the "meet the team" section

If a former member does not have an UU profile, we may add a linkt to the GitHub profile instead

MartineDeVos commented 2 years ago

Another point of discussion for the recap (maybe): should the 'technologies' field be limited to technologies/expertise that we as research engineers developed/used, or should it rather be a list of keywords describing the project?

I would be in favour of keywords. Technologies are surely interesting to mention but may be to limited to describe the topic (for example sensitive data or workflow/pipeline) of a project.

jelletreep commented 2 years ago

I would prefer technologies/expertise that we as research engineers developed/used, as the next field is a short project description, so if we describe the project in keywords that is double. In the former case you can provide 'new' info in the technology field. Although i think the examples "sensitive data" and "pipeline" are great to add as "technology". We could talk about this further during the recap

jelletreep commented 2 years ago 
| [Animal Sounds](https://github.com/UtrechtUniversity/animal-sounds) | 
| --- | 
| 2019-2021 |
| Faculty of Science |
| Technologies: bioacoustics, audio, librosa, machine learning, deep learning, feature engineering | 
| RSEs: [Jelle Treep](https://www.uu.nl/staff/HJTreep), [Parisa Zahedi](https://www.uu.nl/staff/PZahedi), Casper Kaandorp |
| We developed algorithms and a data processing workflow to detect vocalizations of Chimpanzees in a large body of audio data from the African tropical rainforest. The workflow consists of: 1) a filtering step where irrelevant audio data is removed to speed up manual annotation, 2) a feature engineering and feature selection step, and 3) classification using support vector machines and convolutional neural networks |
hailihu commented 2 years ago 
| [Data Donation - proof of concept](https://github.com/eyra/port-poc) | 
| --- | 
| 04/2021-10/2021 |
| Faculty of Social Sciences, Human Data Science group |
| Technologies: Python, WebAssembly, Pyodide, Data Faker | 
| Research Engineers: Haili Hu, Roos Voorvaart |
| In this project, we collaborated with the [Human Data Science group](https://hds.sites.uu.nl/) and [Eyra](https://www.eyra.co/) to make data from social media platforms easily accessible to researchers, while preserving privacy. Respondents can voluntary donate their data download packages through an online platform (PORT), and researchers can provide custom data extraction scripts, which will be run locally on the respondent’s devices. A proof-of-concept PORT has been developed by Eyra, while data extraction scripts and fake data packages were provided by the Research Engineering team.|
hailihu commented 2 years ago 
| [Precision Nudging](https://github.com/UtrechtUniversity/nudging) | 
| --- | 
| 04/2021- |
| Faculty of Law, Economics and Governance, Public Governance and Management |
| Technologies: Python, scikit-learn, data simulation | 
| Research Engineers: [Haili Hu](uu.nl/staff/HHu2), Raoul Schram|
| Changing behavior is necessary to tackle societal problems, such as obesity and financial problems. One way to change behavior is by nudging people. A nudge is a way to change behavior without prohibiting options or changing its costs. However, nudges are often one-size-fits-all techniques: everyone is offered the same nudge. The scientific aim of this project is to use open data to develop predictive models with Machine Learning, in order to determine the most effective nudge for persons, given the nudging goal and the individual personal circumstances.|
MartineDeVos commented 2 years ago
Data Donation - proof of concept
04/2021-10/2021
Faculty of Social Sciences, Human Data Science group
Technologies: Python, WebAssembly, Pyodide, Data Faker
Research Engineers: Haili Hu, Roos Voorvaart
In this project, we collaborated with the Human Data Science group and Eyra to make data from social media platforms easily accessible to researchers, while preserving privacy. Respondents can voluntary donate their data download packages through an online platform (PORT), and researchers can provide custom data extraction scripts, which will be run locally on the respondent’s devices. A proof-of-concept PORT has been developed by Eyra, while data extraction scripts and fake data packages were provided by the Research Engineering team. 

@hailihu  you could add your publication as an additional item
MartineDeVos commented 2 years ago 

| [Global Goals](https://github.com/UtrechtUniversity/global-goals) | 
| --- | 
| 10/2019-08/2020 |
| Faculty of Geosciences, Global Sustainability Governance|
| Technologies: Webscraping,Python,AWS,terraform| 
| RSEs:[Jelle Treep](https://www.uu.nl/staff/HJTreep),[Martine de Vos](https://www.uu.nl/staff/MgdeVos)|
| The global goals project investigates the effect of the United Nations' Sustainable Development Goals (SDGs) on the global network of intergovernmental organizations. This network is represented by the hyperlinks on the organizations’ websites. We have retrieved the historical - from 2012 up to 2019- hyperlinks for a given set of international organizations via the Internet Archive.| ```
MartineDeVos commented 2 years ago 

| [Data Donation – Anonymize Instagram](https://github.com/UtrechtUniversity/anonymize-ddp) | 
| --- | 
| 01/2020-10/2021 |
| Faculty of Social Sciences, Human Data Science group|
| Technologies: De-identification, Python, detecting and blurring visual content: Pytorch, Imaging Library,EAST model,OpenCV| 
| RSEs: [Roos Voorvaart](https://github.com/RVoor), [Martine de Vos](https://www.uu.nl/staff/MGdeVos)|
| Publications: [Automatic de-identification of data download packages] 
(Automatic de-identification of data download packages)
[ Open data set for validation](https://zenodo.org/record/4472606#.YaSvDLso9hE)|
| Instagram users can request their personal data in a Data Download Package (DDP). The data in DDPs may be used for social science research,but can be deeply private. To protect the privacy of research participants, we have developed a de-identification algorithm that is able to handle typical characteristics of DDPs.|```
MartineDeVos commented 2 years ago 

| [Crunchbase](https://github.com/UtrechtUniversity/ia-webscraping) | 
| --- | 
| 05/2020- |
| Faculty of Geosciences, Dynamics of Innovation Systems|
| Technologies: Webscraping,Internet Archive,Pipeline,Internet,Python,AWS,Terraform| 
| RSEs:[Casper Kaandorp](),[Martine de Vos](https://www.uu.nl/staff/MgdeVos)|
| The Crunchbase project assesses the sustainability of European startup-companies by analyzing their websites. As the researcher is interested in the pre-Corona situation, we scrape webpages from the Internet Archive. Together with [SURF](https://www.surf.nl/en/custom-cloud-solutions) we have developed a method to set up AWS workflow for collecting and analyzing these webpages.| ```
MartineDeVos commented 2 years ago 

| [SummerFAIR](https://github.com/UtrechtUniversity/anonymize-ddp) | 
| --- | 
| 02/2021- |
| Faculty of Veterinary Medicine, Veterinary Epidemiology |
| Technologies: Semantic Web,Ontologies,RDF,Docker,Python,R| 
| RSEs:[Martine de Vos](https://www.uu.nl/staff/MGdeVos)|
| The summerFAIR project aims to integrate existing data sets on transmission experiments to enable reanalysis and meta-analysis. We have developed a pipeline based to map data to a shared vocabulary, convert them to linked data triples and perform integrated analyses.| ```
MartineDeVos commented 2 years ago 

| [Data privacy](https://github.com/UtrechtUniversity/dataprivacyhandbook) | 
| --- | 
| 10/2021- |
| Research Data Management Support|
| Technologies: GDPR, de-identification, synthetic data, federated analysis| 
| RSEs:[Martine de Vos](https://www.uu.nl/staff/MGdeVos)|
| The Data Privacy Handbook is a guide to handling personal data in scientific research, in line with European data protection and privacy regulations. The handbook provides tips, guidelines but also concrete tools and approaches for researchers to handle sensitive data in their projects.| ```
parisa-zahedi commented 2 years ago
Agri-activism
2019-2020
Faculty of Social Sciences
Technologies: Python, NLP, topic-modeling, network-analysis
RSEs: Parisa Zahedi, Martine de Vos
This project aims to explore the potential of Twitter data in making sense of online debates. More specifically, the focus is on the online manifestation of the anti-Monsanto movement and assess tweets to investigate (1) activists’ behaviors and opinions, (2) the shape of their networks, (3) their organization and leadership, and (4) information diffusion patterns. Monsanto is one of the world’s largest producers of both agrochemicals and genetically modified crop seeds
parisa-zahedi commented 2 years ago
hist-aware
2020-2021
Faculty of Humanities, History and Art History
Technologies: Python, NLP, Deep learning, Huggingface Transformers
RSEs: Leonardo Vida ,Parisa Zahedi
This project makes use of the Delpher archive (delpher.nl/kranten), which is the largest public collection of digitized pages from Dutch historical newspapers. The research team is mining articles’ sentiments, as expressed by the author of the articles, extracting all the relevant Delpher articles around specific topics (i.e. energy) and is currently training natural language processing (NLP) models called Transformers to extract a sufficiently accurate representation of the sentiment of each article. Currently, the team is making use of the period 1960-1995 consisting of around 250.000 articles around the topics chosen.
parisa-zahedi commented 2 years ago
tweet_collector
2021
Faculty of Humanities, Media and Culture Studies
Technologies: Python, searchtweets, elasticsearch/kibana
RSEs: Parisa Zahedi, Roos Voorvaart
Twitter forms a rich source of information for researchers interested in studying 'the public conversation'. The Academic Research product track is designed to serve the needs of the academic research community. It provides researchers with special levels of access to public Twitter data without any cost. This project is aimed to help researchers to use the Academic Research product track to collect tweets of their interest and analyze them.
parisa-zahedi commented 2 years ago
Dynamiek in beeld
2021
ODISSEI Social Data Science Team (SoDa)
Technologies: Shiny
RSEs: Parisa Zahedi, Shiva Nadi
An application that can be used in a clinical setting to score dynamics in empathy. There are some questions to be asked whereafter the results are visualized. The visualization should help the clinician to ask the right questions immediately.
jelletreep commented 2 years ago

I will add the last ones to the list and then will close this issue. New projects can be added using pull requests!

XiaSteverding commented 1 year ago

While I was reviewing articles, suddenly ASReview disappeared. what should I do to get it back without restart my laptop?

qubixes commented 1 year ago

@XiaSteverding I think you're in the wrong place for that question (and for sure in the wrong issue). If you want help with ASReview/you think there is a bug with it, you can try in the official ASReview repository (https://github.com/asreview/asreview/issues). They would probably appreciate it if you are a bit more specific in what happened and what you did.