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Taguette: open-source qualitative data analysis

Rémi Rampin, Vicky Rampin
2021 Journal of Open Source Software  
Rampin et al., (2021). Taguette: open-source qualitative data analysis. Journal of Open Source Software, 6(68), 3522. https://doi.org/10. 21105/joss.03522  ... 
doi:10.21105/joss.03522 fatcat:dfmjxf3hmjh5dawrzhbli34gou

ReproServer: Making Reproducibility Easier and Less Intensive [article]

Remi Rampin, Fernando Chirigati, Vicky Steeves, Juliana Freire
2018 arXiv   pre-print
Reproducibility in the computational sciences has been stymied because of the complex and rapidly changing computational environments in which modern research takes place. While many will espouse reproducibility as a value, the challenge of making it happen (both for themselves and testing the reproducibility of others' work) often outweigh the benefits. There have been a few reproducibility solutions designed and implemented by the community. In particular, the authors are contributors to
more » ... Zip, a tool to enable computational reproducibility by tracing and bundling together research in the environment in which it takes place (e.g. one's computer or server). In this white paper, we introduce a tool for unpacking ReproZip bundles in the cloud, ReproServer. ReproServer takes an uploaded ReproZip bundle (.rpz file) or a link to a ReproZip bundle, and users can then unpack them in the cloud via their browser, allowing them to reproduce colleagues' work without having to install anything locally. This will help lower the barrier to reproducing others' work, which will aid reviewers in verifying the claims made in papers and reusing previously published research.
arXiv:1808.01406v1 fatcat:5soaytavmbbspdc3q3g6ubr5ua

Reproserver: Making Reproducibility Easier And Less Intrusive

Rémi Rampin, Vicky Steeves, Fernando Chirigati, Juliana Freire
2018 Zenodo  
This poster introduces ReproServer, an open source Web application that allows users to reproduce experiments from the comfort of their Web browser. ReproServer leverages ReproZip: users can unpack and interact with ReproZip bundles over the Web, without having to download any software, and finally share persistent links to the unpacked versions, useful for including in publications.
doi:10.5281/zenodo.1455777 fatcat:lxvhlpkow5eblblmswukaccbki

ReproZip

Fernando Chirigati, Rémi Rampin, Dennis Shasha, Juliana Freire
2016 Proceedings of the 2016 International Conference on Management of Data - SIGMOD '16  
We present ReproZip, the recommended packaging tool for the SIGMOD Reproducibility Review. ReproZip was designed to simplify the process of making an existing computational experiment reproducible across platforms, even when the experiment was put together without reproducibility in mind. The tool creates a self-contained package for an experiment by automatically tracking and identifying all its required dependencies. The researcher can share the package with others, who can then use ReproZip
more » ... o unpack the experiment, reproduce the findings on their favorite operating system, as well as modify the original experiment for reuse in new research, all with little effort. The demo will consist of examples of non-trivial experiments, showing how these can be packed in a Linux machine and reproduced on different machines and operating systems. Demo visitors will also be able to pack and reproduce their own experiments.
doi:10.1145/2882903.2899401 dblp:conf/sigmod/ChirigatiRSF16 fatcat:6u7oatt6dnhwtm7p2g676twmhu

Reproducibility, Preservation, and Access to Research with ReproZip and ReproServer

Rémi Rampin, Vicky Steeves, Fernando Chirigati
2019 Zenodo  
The adoption of reproducibility remains low, despite incentives becoming increasingly common in different domains, conferences, and journals. The truth is, reproducibility is technically difficult to achieve due to the complexities of computational environments. To address these technical challenges, we created ReproZip, an open-source tool that packs research along with all the necessary information to reproduce it, including data files, software, OS version, and environment variables.
more » ... ng is then bundled into an .rpz file, which users can use to reproduce the work with ReproUnzip and an unpacker (Docker, Vagrant, and Singularity). The .rpz file is general and contains rich metadata: more unpackers can be added as needed, better guaranteeing long-term preservation. However, installing the unpackers can still be burdensome for secondary users of ReproZip bundles. In this paper, we will discuss how ReproZip and our new tool ReproServer can be used together to facilitate access to well-preserved, reproducible work. ReproServer is a cloud application that allows users to upload or provide a link to a ReproZip bundle, and then interact with/reproduce the contents from the comfort of their browser. Users are then provided a stable link to the unpacked work on ReproServer they can share with reviewers or colleagues.
doi:10.5281/zenodo.3612732 fatcat:7aoeimz7j5bi7otknmryzbppeq

Using ReproZip for Reproducibility and Library Services

Vicky Steeves, Rémi Rampin, Fernando Chirigati
2017 IASSIST Quarterly  
/14 Steeves, Vicky; Rampin, Rémi and Chirigati, Fernando (2018) Using ReproZip for Reproducibility and Library Services, IASSIST Quarterly 42 (1), pp. 1-14.  ...  DOI https://doi.org/10.29173/iq18 /14 Steeves, Vicky; Rampin, Rémi and Chirigati, Fernando (2018) Using ReproZip for Reproducibility and Library Services, IASSIST Quarterly 42 (1), pp. 1-14.  ... 
doi:10.29173/iq18 fatcat:oj4o6wbelvg7tofm5rf6d2q6tu

ReproZip: The Reproducibility Packer

Rémi Rampin, Fernando Chirigati, Dennis Shasha, Juliana Freire, Vicky Steeves
2016 Journal of Open Source Software  
We have extensive documentation (Rémi Rampin, n.d.), a website visually explaining ReproZip (V. S.  ...  Fernando Chirigati Rémi Rampin 2016), and available examples (Vicky Steeves 2016) with explicit instructions on how to reproduce a subset of use cases.  ...  Fernando Chirigati Rémi Rampin 2016), and available examples (Vicky Steeves 2016) with explicit instructions on how to reproduce a subset of use cases.  ... 
doi:10.21105/joss.00107 fatcat:zt342gtv3vg7hob3vz45to5nwi

Reproducibility, preservation, and access to research with ReproZip and ReproServer

Vicky Steeves, Rémi Rampin, Fernando Chirigati
2020 IASSIST Quarterly  
/11 Steeves, Vicky; Rampin, Rémi; Chirigati, Fernando (2020) Reproducibility, preservation, and access to research with ReproZip and ReproServer, IASSIST Quarterly 44 (1) (2) , pp. 1-11.  ...  DOI: https://doi.org/10.29173/iq969 /11 Steeves, Vicky; Rampin, Rémi; Chirigati, Fernando (2020) Reproducibility, preservation, and access to research with ReproZip and ReproServer, IASSIST Quarterly  ... 
doi:10.29173/iq969 fatcat:bygje7b4s5gqpo4et7qix5ie2i

Auctus: A Dataset Search Engine for Data Augmentation [article]

Sonia Castelo, Rémi Rampin, Aécio Santos, Aline Bessa, Fernando Chirigati, Juliana Freire
2021 arXiv   pre-print
The large volumes of structured data currently available, from Web tables to open-data portals and enterprise data, open up new opportunities for progress in answering many important scientific, societal, and business questions. However, finding relevant data is difficult. While search engines have addressed this problem for Web documents, there are many new challenges involved in supporting the discovery of structured data. We demonstrate how the Auctus dataset search engine addresses some of
more » ... hese challenges. We describe the system architecture and how users can explore datasets through a rich set of queries. We also present case studies which show how Auctus supports data augmentation to improve machine learning models as well as to enrich analytics.
arXiv:2102.05716v2 fatcat:juyw3tujmjcdffbni3z5yls4pm

A collaborative approach to computational reproducibility

Fernando Chirigati, Rebecca Capone, Rémi Rampin, Juliana Freire, Dennis Shasha
2016 Information Systems  
Although a standard in natural science, reproducibility has been only episodically applied in experimental computer science. Scientific papers often present a large number of tables, plots and pictures that summarize the obtained results, but then loosely describe the steps taken to derive them. Not only can the methods and the implementation be complex, but also their configuration may require setting many parameters and/or depend on particular system configurations. While many researchers
more » ... gnize the importance of reproducibility, the challenge of making it happen often outweigh the benefits. Fortunately, a plethora of reproducibility solutions have been recently designed and implemented by the community. In particular, packaging tools (e.g., ReproZip) and virtualization tools (e.g., Docker) are promising solutions towards facilitating reproducibility for both authors and reviewers. To address the incentive problem, we have implemented a new publication model for the Reproducibility Section of Information Systems Journal. In this section, authors submit a reproducibility paper that explains in detail the computational assets from a previous published manuscript in Information Systems.
doi:10.1016/j.is.2016.03.002 fatcat:axuffobgoje2fco6uyaemcamhy

Pooch: A friend to fetch your data files

Leonardo Uieda, Santiago Soler, Rémi Rampin, Hugo van Kemenade, Matthew Turk, Daniel Shapero, Anderson Banihirwe, John Leeman
2020 Journal of Open Source Software  
doi:10.21105/joss.01943 fatcat:4z272rpvljambm5wcqm5f646he

Indication of Cross-Species Transmission of Astrovirus Associated with Encephalitis in Sheep and Cattle

Céline L. Boujon, Michel C. Koch, Daniel Wüthrich, Simea Werder, Dennis Jakupovic, Rémy Bruggmann, Torsten Seuberlich
2017 Emerging Infectious Diseases  
Manarolla G, Pisoni G, Sironi G, Rampin T. Molecular biological characterization of avian poxvirus strains isolated from different avian species.  ... 
doi:10.3201/eid2309.170168 pmid:28820378 pmcid:PMC5572871 fatcat:bfbcpvajrbfphnr3e4ttup6shy

Solving Constrained CASH Problems with ADMM [article]

Parikshit Ram, Sijia Liu, Deepak Vijaykeerthi, Dakuo Wang, Djallel Bouneffouf, Greg Bramble, Horst Samulowitz, Alexander G. Gray
2020 arXiv   pre-print
Iddo Drori, Yamuna Krishnamurthy, Remi Rampin, Raoni Lourenço, J One, Kyunghyun Cho, Claudio Silva, and Juliana Freire. Alphad3m: Machine learning pipeline synthesis.  ...  CASH can be stated as 1 : James S Bergstra, Rémi Bardenet, Yoshua Bengio, and Balázs Kégl. Algorithms for hyper-parameter optimization.  ... 
arXiv:2006.09635v2 fatcat:ldiqvg57bjah7lvu56rbz5u5j4

Noradrenergic Mechanisms in Parkinson's Disease and L-DOPA-Induced Dyskinesia: Hypothesis and Evidences from Behavioural and Biochemical Studies [chapter]

Amal Alachkar
2012 Mechanisms in Parkinson's Disease - Models and Treatments  
body temperature (Lin et al, 1981 , Sallinen et al, 1997 , endocrine secretion (Endroczi et al, 1978; Valet et al, 1989; Ruffolo et al, 1991) , and sexual behaviour (Morales et al, 1987; Guiliano & Rampin  ...  Administration of α 2 -adrenergic agonist was demonstrated to improve the cognitive impairments in PD patients (Remy et al., 2005; Riekkinen and Riekkinen, 1999) .  ... 
doi:10.5772/17435 fatcat:tkr7zd6hzfflvoqs7zyzjmk73q

Page 180 of Psychological Abstracts Vol. 90, Issue Author & Book Title Index [page]

Psychological Abstracts  
., 25275 Quirion, Rémi, 7271, 15669. 24677 Quirk, Alan, 23477 Quirk, Gregory J., 6140, 25432 Quirk, Stuart W., 13580 Quiroa, Ruth E., 24834 Quiroz, Stacy E., 16478 Quisenberry, Neil, 31310 Quist, Raymond  ...  J., 503 Ramos, Kathleen D., 21139 Ramos, Marilia, 31712 Ramos, Sara Isabel, 23126 Ramos-Zepeda, R., 28551 Ramoz, Gina, 9251 Rampage, Cheryl, 16024, 26266 Rampes, Hagen, 35339 Rampichini, Carla, 24258 Rampin  ... 
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