Open Access Week 2017: October 23-27. #oaweek #openaccess #OpenScience
Open Access Week: Version-Controlled Papers. Synthetic Daisies blog.
Open Access Week: Open Project Management. Synthetic Daisies blog.
OpenData Day 2017: March 4. #OpenData #OpenDataDay2017 #OpenDataHack
Open Data Day Activities. Synthetic Daisies blog.
Open Access Week 2016: October 24-28. #oaweek #openaccess #OpenScience
Open Access Week: How Am I Doing, Altmetrics? Synthetic Daisies blog.
Open Access Week: Working with Secondary Datasets. Synthetic Daisies blog.
Open Access Week: Version-Controlled Papers. Synthetic Daisies blog.
Open Access Week: Open Project Management. Synthetic Daisies blog.
OpenData Day 2017: March 4. #OpenData #OpenDataDay2017 #OpenDataHack
Open Data Day Activities. Synthetic Daisies blog.
Open Access Week 2016: October 24-28. #oaweek #openaccess #OpenScience
Open Access Week: How Am I Doing, Altmetrics? Synthetic Daisies blog.
Open Access Week: Working with Secondary Datasets. Synthetic Daisies blog.
Please see our project slack channel for more information: Open Science at Orthogonal Lab Slack.
Open Science Theory Project Page ResearchGate
Open Science Theory Project Page ResearchGate
Innovations/Papers:
Data Reuse as a Prisoner's Dilemma: the social capital of open science. bioRxiv, doi:10.1101/093518 (2016).
A Semi-automated Peer-review System. arXiv, 1311.2504 (2013).
Advent of an Organization-wide Open Science System. Orthogonal Research website.
The Authorship Tree. Figshare, doi:10.6084/m9.figshare.4731913 (2017).
Data Reuse as a Prisoner's Dilemma: the social capital of open science. bioRxiv, doi:10.1101/093518 (2016).
A Semi-automated Peer-review System. arXiv, 1311.2504 (2013).
Advent of an Organization-wide Open Science System. Orthogonal Research website.
The Authorship Tree. Figshare, doi:10.6084/m9.figshare.4731913 (2017).
Lectures:
Theory-building for Data Science. slides
Open Data Science and Theory. Data Science User Group, University of Illinois Research Park. slides
The Role of Web 2.0 Tools and Digital Practice in Doing Open-Science. Webmaster Workshop, University of Illinois Urbana-Champaign. slides video
Theory-building for Data Science. slides
Open Data Science and Theory. Data Science User Group, University of Illinois Research Park. slides
The Role of Web 2.0 Tools and Digital Practice in Doing Open-Science. Webmaster Workshop, University of Illinois Urbana-Champaign. slides video
Secondary datasets (re-analysis):
Open software and secondary datasets from DevoWorm.
Secondary data and analysis from Alicea, B. and Cibelli, J.B. (2013). "Comparing indirect-derived ES cells and directly-derived iPS cells" In "Principles of Cloning", 2nd edition. Elsevier. dataset
Open software and secondary datasets from DevoWorm.
Secondary data and analysis from Alicea, B. and Cibelli, J.B. (2013). "Comparing indirect-derived ES cells and directly-derived iPS cells" In "Principles of Cloning", 2nd edition. Elsevier. dataset
Primary Datasets:
Reproductive Capacity, Developmental Plasticity, and Evolution in C. elegans (B. Alicea). Archived at Figshare, doi:10.1101 /m9.figshare.045609. Referenced in: Alicea, B. Genotype-specific developmental plasticity shapes the timing and robustness of reproductive capacity in Caenorhabditis elegans (bioRxiv, doi:10.1101/045609).
Experimental Evolution Datasets (C. elegans wildtype and mutant genotypes) (B. Alicea). Archived at Figshare, doi:10.6084/ m9.figshare.2087719. Referenced in: Alicea, B. Evolution in Eggs and Phases: experimental evolution of fecundity and reproductive timing in Caenorhabditis elegans (bioRxiv, doi:10.1101/042143)
Mechanism Alteration Reveals Patterns of Cellular Information Processing (B. Alicea). Archived at Figshare, doi: 10.6084/m9.figshare.689894. Referenced in: Modeling Cellular Information Processing Using a Dynamical Approximation of Cellular mRNA (bioRxiv, doi: 10.1101/006775) and Using Polysome Isolation with Mechanism Alteration to Uncover Transcriptional and Translational Dynamics in Key Genes (bioRxiv, doi:10.1101/006213).
Fibroblast Reprogramming Diversity (B. Alicea, S.T. Suhr and S.A. Keaton). Archived at Figshare, doi:10.6084/m9.figshare. 1320528. References in: Defining phenotypic respecification diversity using multiple cell lines and reprogramming regimens. Stem Cells and Development, 22(19), 2641-2654 (2013) and Cellular decision-making bias: the missing ingredient in cell functional diversity. arXiv:1310.8268 (2013).
Worst Performers, Best Predictors (B. Alicea). Archived at Figshare, doi:10.6084/m9.figshare.944542. Referenced in: Are the Worst Performers the Best Predictors? (Synthetic Daisies blog, February 26, 2014) and From Worst to Most Variable? Only the worst performers may be the most informative (Figshare, doi:10.6084/m9.figshare.1015759).
Physical Intelligence Experiments (B. Alicea). Archived at Figshare, doi:10.6084/m9. figshare.1320529. Referenced in: Range-based techniques for discovering optimality and analyzing scaling relationships in neuromechanical systems. Nature Precedings, 2845.v1 (2009) and Performance augmentation in hybrid bionic systems: techniques and experiment. arXiv:0810.4629 (2008) and Naturally Supervised Learning in Manipulable Technologies. arXiv:1106.1105 (2011).
Reproductive Capacity, Developmental Plasticity, and Evolution in C. elegans (B. Alicea). Archived at Figshare, doi:10.1101 /m9.figshare.045609. Referenced in: Alicea, B. Genotype-specific developmental plasticity shapes the timing and robustness of reproductive capacity in Caenorhabditis elegans (bioRxiv, doi:10.1101/045609).
Experimental Evolution Datasets (C. elegans wildtype and mutant genotypes) (B. Alicea). Archived at Figshare, doi:10.6084/ m9.figshare.2087719. Referenced in: Alicea, B. Evolution in Eggs and Phases: experimental evolution of fecundity and reproductive timing in Caenorhabditis elegans (bioRxiv, doi:10.1101/042143)
Mechanism Alteration Reveals Patterns of Cellular Information Processing (B. Alicea). Archived at Figshare, doi: 10.6084/m9.figshare.689894. Referenced in: Modeling Cellular Information Processing Using a Dynamical Approximation of Cellular mRNA (bioRxiv, doi: 10.1101/006775) and Using Polysome Isolation with Mechanism Alteration to Uncover Transcriptional and Translational Dynamics in Key Genes (bioRxiv, doi:10.1101/006213).
Fibroblast Reprogramming Diversity (B. Alicea, S.T. Suhr and S.A. Keaton). Archived at Figshare, doi:10.6084/m9.figshare. 1320528. References in: Defining phenotypic respecification diversity using multiple cell lines and reprogramming regimens. Stem Cells and Development, 22(19), 2641-2654 (2013) and Cellular decision-making bias: the missing ingredient in cell functional diversity. arXiv:1310.8268 (2013).
Worst Performers, Best Predictors (B. Alicea). Archived at Figshare, doi:10.6084/m9.figshare.944542. Referenced in: Are the Worst Performers the Best Predictors? (Synthetic Daisies blog, February 26, 2014) and From Worst to Most Variable? Only the worst performers may be the most informative (Figshare, doi:10.6084/m9.figshare.1015759).
Physical Intelligence Experiments (B. Alicea). Archived at Figshare, doi:10.6084/m9. figshare.1320529. Referenced in: Range-based techniques for discovering optimality and analyzing scaling relationships in neuromechanical systems. Nature Precedings, 2845.v1 (2009) and Performance augmentation in hybrid bionic systems: techniques and experiment. arXiv:0810.4629 (2008) and Naturally Supervised Learning in Manipulable Technologies. arXiv:1106.1105 (2011).
