diff --git a/tutorials/W1D1_TheEthosOfOpenScience/W1D1_Tutorial1.ipynb b/tutorials/W1D1_TheEthosOfOpenScience/W1D1_Tutorial1.ipynb index d3aa73b0..4ac617c2 100644 --- a/tutorials/W1D1_TheEthosOfOpenScience/W1D1_Tutorial1.ipynb +++ b/tutorials/W1D1_TheEthosOfOpenScience/W1D1_Tutorial1.ipynb @@ -437,7 +437,7 @@ "\n", "- [Sweeney and Clopath, 2020](https://elifesciences.org/articles/56053) used Allen Brain Observatory two-photon imaging data to explore the stability of neural responses over time. The authors found that, indeed, population coupling is correlated with the change in orientation and direction tuning of neurons over the course of a single experiment, an unexpected result linking population activity with individual neural responses.\n", "- [Bakhtiari et al., 2021](https://www.biorxiv.org/content/10.1101/2021.06.18.448989v3) examined whether a deep artificial neural network (ANN) could model both the ventral and dorsal pathways of the visual system in a single network with a single cost function. Comparing the representations of these networks with the neural responses in the two-photon imaging dataset, they found that the single pathway produced ventral-like representations but failed to capture the representational similarity of the dorsal areas.\n", - "- [Fritsche et al., 2022](https://www.jneurosci.org/content/42/10/1999) analyzed the time course of stimulus-specific adaptation in 2365 neurons in the Neuropixels dataset and discovered that a single presentation of a drifting or static grating in a specific orientation leads to a reduction in the response to the same visual stimulus up to eight trials (22 s) in the future. This stimulus-specific, long-term adaptation persists despite intervening stimuli, and is seen in all six visual cortical areas, but not in visual thalamic areas (LGN and LP), which returned to baseline after one or two trials. This is a remarkable example of a discovery that was not envisioned when designing our survey, but for which our stimulus set was well suited.\n", + "- [Fritsche et al., 2022](https://www.jneurosci.org/content/42/10/1999) analyzed the time course of stimulus-specific adaptation in 2365 neurons in the Neuropixels dataset and discovered that a single presentation of a drifting or static grating in a specific orientation leads to a reduction in the response to the same visual stimulus up to eight trials (22 s) in the future. This stimulus-specific, long-term adaptation persists despite intervening stimuli, and is seen in all six visual cortical areas, but not in visual thalamic areas (LGN and LP), which returned to baseline after one or two trials. This is a remarkable example of a discovery that was not envisioned when designing the survey, but for which the stimulus set was well suited.\n", "\n", "*Information on the case study is taken from 2023 [article](https://elifesciences.org/articles/85550).*\n", "\n", diff --git a/tutorials/W1D1_TheEthosOfOpenScience/instructor/W1D1_Tutorial1.ipynb b/tutorials/W1D1_TheEthosOfOpenScience/instructor/W1D1_Tutorial1.ipynb index d3aa73b0..4ac617c2 100644 --- a/tutorials/W1D1_TheEthosOfOpenScience/instructor/W1D1_Tutorial1.ipynb +++ b/tutorials/W1D1_TheEthosOfOpenScience/instructor/W1D1_Tutorial1.ipynb @@ -437,7 +437,7 @@ "\n", "- [Sweeney and Clopath, 2020](https://elifesciences.org/articles/56053) used Allen Brain Observatory two-photon imaging data to explore the stability of neural responses over time. The authors found that, indeed, population coupling is correlated with the change in orientation and direction tuning of neurons over the course of a single experiment, an unexpected result linking population activity with individual neural responses.\n", "- [Bakhtiari et al., 2021](https://www.biorxiv.org/content/10.1101/2021.06.18.448989v3) examined whether a deep artificial neural network (ANN) could model both the ventral and dorsal pathways of the visual system in a single network with a single cost function. Comparing the representations of these networks with the neural responses in the two-photon imaging dataset, they found that the single pathway produced ventral-like representations but failed to capture the representational similarity of the dorsal areas.\n", - "- [Fritsche et al., 2022](https://www.jneurosci.org/content/42/10/1999) analyzed the time course of stimulus-specific adaptation in 2365 neurons in the Neuropixels dataset and discovered that a single presentation of a drifting or static grating in a specific orientation leads to a reduction in the response to the same visual stimulus up to eight trials (22 s) in the future. This stimulus-specific, long-term adaptation persists despite intervening stimuli, and is seen in all six visual cortical areas, but not in visual thalamic areas (LGN and LP), which returned to baseline after one or two trials. This is a remarkable example of a discovery that was not envisioned when designing our survey, but for which our stimulus set was well suited.\n", + "- [Fritsche et al., 2022](https://www.jneurosci.org/content/42/10/1999) analyzed the time course of stimulus-specific adaptation in 2365 neurons in the Neuropixels dataset and discovered that a single presentation of a drifting or static grating in a specific orientation leads to a reduction in the response to the same visual stimulus up to eight trials (22 s) in the future. This stimulus-specific, long-term adaptation persists despite intervening stimuli, and is seen in all six visual cortical areas, but not in visual thalamic areas (LGN and LP), which returned to baseline after one or two trials. This is a remarkable example of a discovery that was not envisioned when designing the survey, but for which the stimulus set was well suited.\n", "\n", "*Information on the case study is taken from 2023 [article](https://elifesciences.org/articles/85550).*\n", "\n", diff --git a/tutorials/W1D1_TheEthosOfOpenScience/student/W1D1_Tutorial1.ipynb b/tutorials/W1D1_TheEthosOfOpenScience/student/W1D1_Tutorial1.ipynb index d3aa73b0..4ac617c2 100644 --- a/tutorials/W1D1_TheEthosOfOpenScience/student/W1D1_Tutorial1.ipynb +++ b/tutorials/W1D1_TheEthosOfOpenScience/student/W1D1_Tutorial1.ipynb @@ -437,7 +437,7 @@ "\n", "- [Sweeney and Clopath, 2020](https://elifesciences.org/articles/56053) used Allen Brain Observatory two-photon imaging data to explore the stability of neural responses over time. The authors found that, indeed, population coupling is correlated with the change in orientation and direction tuning of neurons over the course of a single experiment, an unexpected result linking population activity with individual neural responses.\n", "- [Bakhtiari et al., 2021](https://www.biorxiv.org/content/10.1101/2021.06.18.448989v3) examined whether a deep artificial neural network (ANN) could model both the ventral and dorsal pathways of the visual system in a single network with a single cost function. Comparing the representations of these networks with the neural responses in the two-photon imaging dataset, they found that the single pathway produced ventral-like representations but failed to capture the representational similarity of the dorsal areas.\n", - "- [Fritsche et al., 2022](https://www.jneurosci.org/content/42/10/1999) analyzed the time course of stimulus-specific adaptation in 2365 neurons in the Neuropixels dataset and discovered that a single presentation of a drifting or static grating in a specific orientation leads to a reduction in the response to the same visual stimulus up to eight trials (22 s) in the future. This stimulus-specific, long-term adaptation persists despite intervening stimuli, and is seen in all six visual cortical areas, but not in visual thalamic areas (LGN and LP), which returned to baseline after one or two trials. This is a remarkable example of a discovery that was not envisioned when designing our survey, but for which our stimulus set was well suited.\n", + "- [Fritsche et al., 2022](https://www.jneurosci.org/content/42/10/1999) analyzed the time course of stimulus-specific adaptation in 2365 neurons in the Neuropixels dataset and discovered that a single presentation of a drifting or static grating in a specific orientation leads to a reduction in the response to the same visual stimulus up to eight trials (22 s) in the future. This stimulus-specific, long-term adaptation persists despite intervening stimuli, and is seen in all six visual cortical areas, but not in visual thalamic areas (LGN and LP), which returned to baseline after one or two trials. This is a remarkable example of a discovery that was not envisioned when designing the survey, but for which the stimulus set was well suited.\n", "\n", "*Information on the case study is taken from 2023 [article](https://elifesciences.org/articles/85550).*\n", "\n", diff --git a/tutorials/W1D2_OpenToolsAndResources/W1D2_Tutorial1.ipynb b/tutorials/W1D2_OpenToolsAndResources/W1D2_Tutorial1.ipynb index 308026d4..c6dc430a 100644 --- a/tutorials/W1D2_OpenToolsAndResources/W1D2_Tutorial1.ipynb +++ b/tutorials/W1D2_OpenToolsAndResources/W1D2_Tutorial1.ipynb @@ -614,7 +614,7 @@ "execution": {} }, "source": [ - "## Introduction to Open Data\n", + "### Introduction to Open Data\n", "\n", "Scientific data is any type of information that is collected, observed, or created in the context of research. It can be:\n", "\n", @@ -627,7 +627,7 @@ "\n", "The following sections discuss ways to ensure that data is fully utilized and accessible to the most amount of people. These best practices center around community frameworks and tools that help researchers manage and share open data.\n", "\n", - "## FAIR Principles\n", + "### FAIR Principles\n", " \n", "Just like driving on the road, if everyone follows agreed-upon rules, everything goes much smoother. The rules don’t need to be exactly the same for every region but share common practices based on insights about safety and efficiency.\n", "\n", diff --git a/tutorials/W1D2_OpenToolsAndResources/instructor/W1D2_Tutorial1.ipynb b/tutorials/W1D2_OpenToolsAndResources/instructor/W1D2_Tutorial1.ipynb index 308026d4..c6dc430a 100644 --- a/tutorials/W1D2_OpenToolsAndResources/instructor/W1D2_Tutorial1.ipynb +++ b/tutorials/W1D2_OpenToolsAndResources/instructor/W1D2_Tutorial1.ipynb @@ -614,7 +614,7 @@ "execution": {} }, "source": [ - "## Introduction to Open Data\n", + "### Introduction to Open Data\n", "\n", "Scientific data is any type of information that is collected, observed, or created in the context of research. It can be:\n", "\n", @@ -627,7 +627,7 @@ "\n", "The following sections discuss ways to ensure that data is fully utilized and accessible to the most amount of people. These best practices center around community frameworks and tools that help researchers manage and share open data.\n", "\n", - "## FAIR Principles\n", + "### FAIR Principles\n", " \n", "Just like driving on the road, if everyone follows agreed-upon rules, everything goes much smoother. The rules don’t need to be exactly the same for every region but share common practices based on insights about safety and efficiency.\n", "\n", diff --git a/tutorials/W1D2_OpenToolsAndResources/static/image5.png b/tutorials/W1D2_OpenToolsAndResources/static/image5.png index 7b71f0e7..d9ca2ca9 100644 Binary files a/tutorials/W1D2_OpenToolsAndResources/static/image5.png and b/tutorials/W1D2_OpenToolsAndResources/static/image5.png differ diff --git a/tutorials/W1D2_OpenToolsAndResources/static/image6.png b/tutorials/W1D2_OpenToolsAndResources/static/image6.png index 45601965..2f4f269c 100644 Binary files a/tutorials/W1D2_OpenToolsAndResources/static/image6.png and b/tutorials/W1D2_OpenToolsAndResources/static/image6.png differ diff --git a/tutorials/W1D2_OpenToolsAndResources/static/image7.png b/tutorials/W1D2_OpenToolsAndResources/static/image7.png index 20d48ac4..ad0bfc8a 100644 Binary files a/tutorials/W1D2_OpenToolsAndResources/static/image7.png and b/tutorials/W1D2_OpenToolsAndResources/static/image7.png differ diff --git a/tutorials/W1D2_OpenToolsAndResources/student/W1D2_Tutorial1.ipynb b/tutorials/W1D2_OpenToolsAndResources/student/W1D2_Tutorial1.ipynb index 308026d4..c6dc430a 100644 --- a/tutorials/W1D2_OpenToolsAndResources/student/W1D2_Tutorial1.ipynb +++ b/tutorials/W1D2_OpenToolsAndResources/student/W1D2_Tutorial1.ipynb @@ -614,7 +614,7 @@ "execution": {} }, "source": [ - "## Introduction to Open Data\n", + "### Introduction to Open Data\n", "\n", "Scientific data is any type of information that is collected, observed, or created in the context of research. It can be:\n", "\n", @@ -627,7 +627,7 @@ "\n", "The following sections discuss ways to ensure that data is fully utilized and accessible to the most amount of people. These best practices center around community frameworks and tools that help researchers manage and share open data.\n", "\n", - "## FAIR Principles\n", + "### FAIR Principles\n", " \n", "Just like driving on the road, if everyone follows agreed-upon rules, everything goes much smoother. The rules don’t need to be exactly the same for every region but share common practices based on insights about safety and efficiency.\n", "\n", diff --git a/tutorials/W1D3_OpenData/W1D3_Tutorial1.ipynb b/tutorials/W1D3_OpenData/W1D3_Tutorial1.ipynb index 39a9cd1f..95a738a4 100644 --- a/tutorials/W1D3_OpenData/W1D3_Tutorial1.ipynb +++ b/tutorials/W1D3_OpenData/W1D3_Tutorial1.ipynb @@ -1128,7 +1128,7 @@ "\n", "*Estimated time for activity: 15 minutes*\n", "\n", - "Take a look at the examples of a public data management plan from [New Jersey Institute of Technology](https://dmptool.org/plans/102783/export.pdf?export%5Bpub%5D=true&export%5Bquestion_headings%5D=true) and from [University of California San Diego](https://library.ucsd.edu/research-and-collections/research-data/_files/dmpsample/DMP-Example-Psych.doc).\n", + "Take a look at the examples of a public data management plan from [University of North Carolina at Chapel Hill](https://dmptool.org/plans/113336/export.pdf?export%5Bpub%5D=true&export%5Bquestion_headings%5D=true) and from [University of California San Diego](https://library.ucsd.edu/research-and-collections/research-data/_files/dmpsample/DMP-Example-Psych.doc).\n", "\n", "If direct link for the University of California San Diego doesn't work for you, please visit the [following link](https://library.ucsd.edu/research-and-collections/research-data/plan-and-manage/sample-nsf-data-management-plans.html), scroll to the end of the page and open `DMP Example Psych.doc` document.\n", "\n", diff --git a/tutorials/W1D3_OpenData/instructor/W1D3_Tutorial1.ipynb b/tutorials/W1D3_OpenData/instructor/W1D3_Tutorial1.ipynb index 39a9cd1f..95a738a4 100644 --- a/tutorials/W1D3_OpenData/instructor/W1D3_Tutorial1.ipynb +++ b/tutorials/W1D3_OpenData/instructor/W1D3_Tutorial1.ipynb @@ -1128,7 +1128,7 @@ "\n", "*Estimated time for activity: 15 minutes*\n", "\n", - "Take a look at the examples of a public data management plan from [New Jersey Institute of Technology](https://dmptool.org/plans/102783/export.pdf?export%5Bpub%5D=true&export%5Bquestion_headings%5D=true) and from [University of California San Diego](https://library.ucsd.edu/research-and-collections/research-data/_files/dmpsample/DMP-Example-Psych.doc).\n", + "Take a look at the examples of a public data management plan from [University of North Carolina at Chapel Hill](https://dmptool.org/plans/113336/export.pdf?export%5Bpub%5D=true&export%5Bquestion_headings%5D=true) and from [University of California San Diego](https://library.ucsd.edu/research-and-collections/research-data/_files/dmpsample/DMP-Example-Psych.doc).\n", "\n", "If direct link for the University of California San Diego doesn't work for you, please visit the [following link](https://library.ucsd.edu/research-and-collections/research-data/plan-and-manage/sample-nsf-data-management-plans.html), scroll to the end of the page and open `DMP Example Psych.doc` document.\n", "\n", diff --git a/tutorials/W1D3_OpenData/student/W1D3_Tutorial1.ipynb b/tutorials/W1D3_OpenData/student/W1D3_Tutorial1.ipynb index 39a9cd1f..95a738a4 100644 --- a/tutorials/W1D3_OpenData/student/W1D3_Tutorial1.ipynb +++ b/tutorials/W1D3_OpenData/student/W1D3_Tutorial1.ipynb @@ -1128,7 +1128,7 @@ "\n", "*Estimated time for activity: 15 minutes*\n", "\n", - "Take a look at the examples of a public data management plan from [New Jersey Institute of Technology](https://dmptool.org/plans/102783/export.pdf?export%5Bpub%5D=true&export%5Bquestion_headings%5D=true) and from [University of California San Diego](https://library.ucsd.edu/research-and-collections/research-data/_files/dmpsample/DMP-Example-Psych.doc).\n", + "Take a look at the examples of a public data management plan from [University of North Carolina at Chapel Hill](https://dmptool.org/plans/113336/export.pdf?export%5Bpub%5D=true&export%5Bquestion_headings%5D=true) and from [University of California San Diego](https://library.ucsd.edu/research-and-collections/research-data/_files/dmpsample/DMP-Example-Psych.doc).\n", "\n", "If direct link for the University of California San Diego doesn't work for you, please visit the [following link](https://library.ucsd.edu/research-and-collections/research-data/plan-and-manage/sample-nsf-data-management-plans.html), scroll to the end of the page and open `DMP Example Psych.doc` document.\n", "\n", diff --git a/tutorials/W1D5_OpenResults/W1D5_Tutorial1.ipynb b/tutorials/W1D5_OpenResults/W1D5_Tutorial1.ipynb index 05febc30..a9299c68 100644 --- a/tutorials/W1D5_OpenResults/W1D5_Tutorial1.ipynb +++ b/tutorials/W1D5_OpenResults/W1D5_Tutorial1.ipynb @@ -126,13 +126,7 @@ "\n", "**Scientists can share their incremental progress throughout the research process and invite community feedback. Sharing more parts of the research process creates more interactions between researchers and can improve the end result (which may be a peer-reviewed article).**\n", "\n", - "Throughout this day, we will show you how to use, make, and share open results.\n", - "\n", - "#### The Practice of 'Open'\n", - "\n", - "Specifically, the \"Use, Make, Share\" format has been naturally embedded throughout the curriculum and should be a familiar format by now. Section 2 will cover \"Using\". Section 3 will cover \"Making\". Section 4 will cover \"Sharing\". Throughout this module, we will pay particular attention to manuscripts and other research products as examples because the previous modules covered \"Use, Make, Share\" in the context of components with data and software.\n", - "\n", - "\"Use," + "Throughout this day, we will show you how to use, make, and share open results." ] }, { diff --git a/tutorials/W1D5_OpenResults/instructor/W1D5_Tutorial1.ipynb b/tutorials/W1D5_OpenResults/instructor/W1D5_Tutorial1.ipynb index 05febc30..a9299c68 100644 --- a/tutorials/W1D5_OpenResults/instructor/W1D5_Tutorial1.ipynb +++ b/tutorials/W1D5_OpenResults/instructor/W1D5_Tutorial1.ipynb @@ -126,13 +126,7 @@ "\n", "**Scientists can share their incremental progress throughout the research process and invite community feedback. Sharing more parts of the research process creates more interactions between researchers and can improve the end result (which may be a peer-reviewed article).**\n", "\n", - "Throughout this day, we will show you how to use, make, and share open results.\n", - "\n", - "#### The Practice of 'Open'\n", - "\n", - "Specifically, the \"Use, Make, Share\" format has been naturally embedded throughout the curriculum and should be a familiar format by now. Section 2 will cover \"Using\". Section 3 will cover \"Making\". Section 4 will cover \"Sharing\". Throughout this module, we will pay particular attention to manuscripts and other research products as examples because the previous modules covered \"Use, Make, Share\" in the context of components with data and software.\n", - "\n", - "\"Use," + "Throughout this day, we will show you how to use, make, and share open results." ] }, { diff --git a/tutorials/W1D5_OpenResults/student/W1D5_Tutorial1.ipynb b/tutorials/W1D5_OpenResults/student/W1D5_Tutorial1.ipynb index 05febc30..a9299c68 100644 --- a/tutorials/W1D5_OpenResults/student/W1D5_Tutorial1.ipynb +++ b/tutorials/W1D5_OpenResults/student/W1D5_Tutorial1.ipynb @@ -126,13 +126,7 @@ "\n", "**Scientists can share their incremental progress throughout the research process and invite community feedback. Sharing more parts of the research process creates more interactions between researchers and can improve the end result (which may be a peer-reviewed article).**\n", "\n", - "Throughout this day, we will show you how to use, make, and share open results.\n", - "\n", - "#### The Practice of 'Open'\n", - "\n", - "Specifically, the \"Use, Make, Share\" format has been naturally embedded throughout the curriculum and should be a familiar format by now. Section 2 will cover \"Using\". Section 3 will cover \"Making\". Section 4 will cover \"Sharing\". Throughout this module, we will pay particular attention to manuscripts and other research products as examples because the previous modules covered \"Use, Make, Share\" in the context of components with data and software.\n", - "\n", - "\"Use," + "Throughout this day, we will show you how to use, make, and share open results." ] }, {