Merge pull request #2 from neuromatch/workflow-fix

Misc: logo and workflow

README.md

@@ -14,7 +14,7 @@
 
 Transform to Open Science (TOPS) is a NASA initiative designed to rapidly transform agencies, organizations, and communities to an inclusive culture of open science. Developed by the TOPS initiative, the guidance provided by the Open Science curriculum will promote the transformation of the research landscape and the accompanying advancement of scientific discovery. The Open Science curriculum aims to introduce learners to a nuanced understanding of open science, enabling participants to better understand an open science workflow from end to end. The focus of the curriculum will be on providing learners with a basic understanding of open science, its ethos and benefits, and how to actively participate in open science communities. The course consists of 5 modules (each for 1 day of the course) being organized as a scientific workflow.
 
-**TODO**: add image of all modules.
+<img src="https://github.com/neuromatch/nasa-open-science/blob/main/tutorials/W1D1_TheEthosOfOpenScience/static/image441.png?raw=true" style="width:100%; height: auto;" alt = "All 5 modules"/>
 
 A NASA Open Science digital badge is earned by completing all five modules and passing the assessment at the end of each day.
 

book/_config.yml

@@ -5,10 +5,10 @@
 
 #######################################################################################
 # Book settings
-title                       : "Insert your title here. e.g. Neuromatch Academy: Computational Neuroscience"  # The title of the book. Will be placed in the left navbar.
+title                       : "Open Science Course"  # The title of the book. Will be placed in the left navbar.
 author                      : Neuromatch  # The author of the book
 copyright                   : ""  # Copyright year to be placed in the footer
-logo                        : tutorials/static/nma-logo-square-4xp.png  # A path to the book logo
+logo                        : tutorials/static/tops.png  # A path to the book logo
 only_build_toc_files        : true
 
 
@@ -69,6 +69,6 @@ launch_buttons:
   colab_url                 : "" # The URL of Google Colab (https://colab.research.google.com)
 
 repository:
-  url                       : https://github.com/neuromatch/course-content-template  # The URL to your book's repository
+  url                       : https://github.com/neuromatch/nasa-open-science  # The URL to your book's repository
   path_to_book              : book  # A path to your book's folder, relative to the repository root.
   branch                    : main  # Which branch of the repository should be used when creating links

tutorials/TechnicalHelp/Discord.md

@@ -0,0 +1,3 @@
+# Using discord
+
+[Please click here for Discord Guide](https://docs.neuromatch.io/p/bz7uXZLMwMvDqn/Discord-Guides)

tutorials/TechnicalHelp/Links_Policy.md

@@ -2,32 +2,26 @@
 
 ## Quick links
 
-Course materials: [https://compneuro.neuromatch.io/](https://compneuro.neuromatch.io/)
+Course materials: [https://neuroai.neuromatch.io/](https://neuroai.neuromatch.io/)
 
 Portal: [https://portal.neuromatchacademy.org/](https://portal.neuromatchacademy.org/)
 
-Website: [https://academy.neuromatch.io/](https://academy.neuromatch.io/)
-
-Crowdcast: [https://www.crowdcast.io/e/neuromatch-academy-2022-](https://www.crowdcast.io/e/neuromatch-academy-2022-)
+Website: [https://neuromatch.io/](https://neuromatch.io/)
 
 Code of Conduct and Code of Conduct Violations Form: [https://github.com/NeuromatchAcademy/precourse/blob/main/CODE_OF_CONDUCT.md](https://github.com/NeuromatchAcademy/precourse/blob/main/CODE_OF_CONDUCT.md)
 
 Project Exemption Form: [https://airtable.com/shrubhlgsWJ8DuA7E](https://airtable.com/shrubhlgsWJ8DuA7E)
 
-Attendance Exemption Form: [https://airtable.com/shrlp9uktPR5o9U28](https://airtable.com/shrlp9uktPR5o9U28)
-
 
 
 ## Policies
 
 ### Coursework attendance policy
 
-Students who participate in this course will gain a certificate of completion for the coursework. Students are allowed to miss two days if necessary and if they communicate that with their teaching assistant.  If there are exceptional circumstances that force a student to miss class for reasons completely beyond their control, such as severe illness, electricity blackouts, etc, they can request to get the certificate despite missing more than two days by filling out the attendance exemption form ([https://airtable.com/shrlp9uktPR5o9U28](https://airtable.com/shrlp9uktPR5o9U28)) **at least two days prior to the end of course**. Please note these requests may not be granted.
+Students who participate in this course will gain a certificate of completion for the coursework. Students are allowed to miss two days if necessary and if they communicate that with their teaching assistant. If there are exceptional circumstances that force a student to miss class for reasons completely beyond their control, such as severe illness, electricity blackouts, etc, they can request to get the certificate despite missing more than two days by filling out the Attendance Waiver ([https://airtable.com/appQ20RmRMNxUVUTd/shrKlQX3PHW8OcTtg](https://airtable.com/appQ20RmRMNxUVUTd/shrKlQX3PHW8OcTtg)) **at least two days prior to the end of course**. Please note these requests may not be granted.
 
 ### Projects attendance policy
 
 Projects are an integral part of the Neuromatch Academy experience. Students who participate in projects and miss no more than two days of projects work will gain a certificate of completion for the projects. 
 
-If there are exceptional circumstances that make it difficult to attend the projects portion of the course, students can request to drop out of projects by filling out the project exemption form ([https://airtable.com/shrubhlgsWJ8DuA7E](https://airtable.com/shrubhlgsWJ8DuA7E)). If their request is granted, the student can continue to attend the coursework sections and gain a coursework certificate if eligible (see above), but not participate in the projects work.
-
-If the student participates in projects but misses more than two days due to exceptional circumstances, they can request to get the projects certificate anyway by filling out the attendance exemption form ([https://airtable.com/shrlp9uktPR5o9U28](https://airtable.com/shrlp9uktPR5o9U28)) **at least two days prior to the end of course**. Please note these requests may not be granted.
+If the student participates in projects but misses more than two days due to exceptional circumstances, they can request to get the projects certificate anyway by filling out the Attendance Waiver ([https://airtable.com/appQ20RmRMNxUVUTd/shrKlQX3PHW8OcTtg](https://airtable.com/appQ20RmRMNxUVUTd/shrKlQX3PHW8OcTtg)) **at least two days prior to the end of course**. Please note these requests may not be granted.

tutorials/W1D1_TheEthosOfOpenScience/further_reading.md

@@ -0,0 +1,45 @@
+## Key terms
+
+**Open Science** – The principle and practice of making research products and processes available to all, while respecting diverse cultures, maintaining security and privacy, and fostering collaborations, reproducibility and equity.
+
+**Open Data** – Data that can be freely used, re-used and redistributed by anyone. Learn more [here](https://opendatahandbook.org/guide/en/what-is-open-data/).
+
+**Open Source** – Computer programs in which the source code is available to the general public for use or modification from its original design. Learn more [here.](https://en.wikipedia.org/wiki/Open_source)
+
+**Open Access** – Free access to information and unrestricted use of electronic resources for everyone. Learn more [here.](https://en.unesco.org/open-access/what-open-access)
+
+**Interdisciplinary** – Combining multiple [academic disciplines](https://en.wikipedia.org/wiki/Academic_discipline) into one activity, such as a research project. Learn more [here.](https://en.wikipedia.org/wiki/Interdisciplinarity)
+
+**Equitable** – Indicates the absence of unfair, avoidable or remediable differences among groups of people, whether those groups are defined socially, economically, demographically, or geographically or by other dimensions of inequality (e.g. sex, gender, ethnicity, disability, or sexual orientation). Learn more [here.](https://www.who.int/health-topics/health-equity)
+
+**Citizen Science, Community Science, and Participatory Science** - Terms used to describe projects where members of the public participate in the scientific process.
+
+- **Citizen Science** is [defined by law](https://www.congress.gov/114/plaws/publ329/PLAW-114publ329.pdf) as "as a form of open collaboration in which individuals or organizations participate voluntarily in the scientific process in various ways". Below is additional information regarding NASA's Citizen Science efforts:
+  - NASA policy [defines citizen science projects](https://smd-cms.nasa.gov/wp-content/uploads/2023/04/SPD_33_Citizen_Science_TAGGED.pdf) as science projects that rely on volunteers.
+  - [NASA's citizen science projects](https://science.nasa.gov/citizen-science/) are held to the same rigorous standards as any NASA science project.
+  - This important ethical practice respects volunteers by helping ensure that their work will result in real contributions to science—ideally published in the scientific literature. You can [learn more here](https://science.nasa.gov/citizen-science/resources/) about leading a NASA citizen science project.
+- **[Community Science](https://calacademy.org/Community-science)** may include projects with or without professional scientists involved.
+- **[Participatory Science](https://serc.si.edu/why-do-we-call-it-participatory-science)**  is another term that avoids using the word "citizen" to avoid confusion and increase inclusiveness, since participation in citizen science and community science projects generally does not require citizenship in any particular country.
+
+**Open Research** – How research is performed and how knowledge is shared based on the principle that research should be as open as possible. Learn more [here.](https://www.ukri.org/what-we-do/supporting-healthy-research-and-innovation-culture/open-research/)
+
+**Open Scholarship** – An expansive term meant to encompass the rapid and widespread sharing of a range of scholarly activities and outputs across multiple disciplines. Learn more [here.](https://www.heliosopen.org/about)
+
+**Reproducibility and Replicability** – Reproducibility is defined as obtaining consistent results using the same data and code as an original study (synonymous with computational reproducibility). Replicability means obtaining consistent results across studies aimed at answering the same scientific question using new data or other new computational methods. Learn more [here.](https://www.nationalacademies.org/news/2019/09/reproducibility-and-replicability-in-research)
+
+**Peer Review** – The evaluation of work by one or more people with similar competencies as the producers of the work - that is, the authors' peers. Learn more [here.](https://en.wikipedia.org/wiki/Peer_review)
+
+**FAIR principles** – Principles to improve the Findability, Accessibility, Interoperability, and Reuse of digital assets. The principles emphasize machine- actionability (i.e., the capacity of computational systems to find, access, interoperate, and reuse data with none or minimal human intervention) because humans increasingly rely on computational support to deal with data as a result of the increase in volume, complexity, and creation speed of data.
+
+**Metrics (in context of scientific merit)** – Quantitative tools used to help assess the quality and impact of research outputs (e.g., scientific articles, researchers, and more). Learn more [here](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8397294/) and [here.](https://editorresources.taylorandfrancis.com/understanding-research-metrics/)
+
+**Altmetrics** – Alternative tools to assess the impact of a scientific article that do not involve journal-level usage information like impact factors.
+Learn more [here.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3792863/)
+
+**Openness** – A concept or personality trait that involves transparency, collaboration, honesty, and receptivity to new ideas and experiences.
+
+**Transparency** – The quality of being easy to perceive or detect.
+
+**Rigor** – Widely used by educators to describe instruction, schoolwork, learning experience, and educational expectations that are academically, intellectually, and personally challenging.
+
+**Computational Provenance** - Seeks to develop systematic, computationally-based processes and standards for capturing, and making available for us, information about who created an object, when it was created or modified, and the process or procedure that modified the object.