@andykrause

In order to have a standard voice throughout the author introductions in the book we made the following change in 3e3807b

Could you please briefly review this?

Also, if you like to have your colleague Hossein Estiri a co-author to the chapter, we can certainly do that too. Then we would change the voice from "I" to "We" in this introductory part. Just let me know.

Hi @garretchristensen, we got some revisions back and there are a few minor points that I would like you to go over:

• Could you please revise the following sentence. It is difficult to read it:
  "I obtained this data from a public Defense Department website, and though I still have, and have archived on Dataverse, the dataset I downloaded and used, perhaps unsurprisingly, the original website is no longer operable."
• Is the last paragraph of your case study perhaps better under Pain Points. It is the pargraph that starts with:
  "I’d say that my code is fairly well-documented. Reading through it, I hope that
  other researchers could understand what the code is doing. [...]"

@kellieotto
Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.

Narrative

• Please read carefully checking for typos or grammatical errors. (e.g. The premise of the method is to predict the outcome of interest, change in life expectancy, as well as possible using all covariates exceptthe treatment of interest, sodium.)
• Please remove starting date of the project, instead we recommend you to state the amount of the time you needed to conduct the study. Project begin is hard to relate in a book.
• Please update the manuscript submission information if necessary (e.g. you mention “A manuscript is in preparation” is this still up to date?)
• Please elaborate the following sentence for a better understanding of your case study: “ Then, if the treatment adds any additional predictive information beyond the covariates, the treatment will be associated with the residuals of the model.”
• As you developed some code we would suggest you to elaborate whether you did some unit testing on the code. If yes, this would be valuable information for the reader.

Diagram

• Please make arrow heads a little bit bigger. They’re tiny! =)
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@gilbertozp
Your case study represents a useful and interesting example of reproducibility for data processing, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.

Narrative

• Please read carefully checking for typos or grammatical errors
• Shorthand DB: change to database
• Can you add any description or information about the specific software and/or tools used for all the data processing tasks you describe? We believe this would really strengthen your case study.

Diagram

• Please add the label “Stage II: Data Processing” to your Diagram, following the examples in CaseStudies123.png as a guideline. This label should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please make all your lines into narrow black lines (as in our example diagram)
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Your case study represents a useful and interesting example of reproducibility in neuroimaging, and we value this contribution. The narrative and diagram are very clear. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please use the word “command line” or “shell prompt”
• Please resolve [citation needed] in the second question

Narrative

• Please read carefully checking for typos or grammatical errors
• Please define the acronym SNR, SDR, API
• Please briefly describe RAID, unit-testing

Diagram

Nothing to add.

Your case study represents a useful and interesting example of reproducibility of archeological data analysis, and we value this contribution. The diagram and narrative are very clear. We’re only requesting the addition of a Title, and some minor revisions to your Narrative and Diagram.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.

Narrative

• Please read carefully checking for typos or grammatical errors
• Please change “other people” to scientists / other researchers
• Please give very brief descriptions for the different licenses (CC0 license, CC-BY license)

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@choldgraf
Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. We’re requesting some minor revisions to your Narrative and Diagram.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.

Narrative

• Please read carefully checking for typos or grammatical errors
• Break down long paragraphs into shorter ideas (throughout entire Narrative).
• Typo in one place, you refer to “fif” file format. I assume you meant “fiff” ?
• Briefly introduce “fiff” file format, Pandas, SGE, HDF5,
• Change “In my field” to “In the field of …”

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please change the one diagnol line so it doesn’t go under another box. Maybe add right angle turns?
  Once these changes are all made, please provide us with both the PDF and editable source file.
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Although they’re cute, please remove the jokes from your diagram: the sad face, and the Nobel Prize, and any others.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@rachelslaybaugh
Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.

Narrative

• Please read carefully checking for typos or grammatical errors.
• Is a 0-dimensional version of an algorithm actually testable? It seems to me reduction to this level is usually totally trivial! Maybe say 1-D version, instead? (but then, I’m totally not familiar with your field =)
• Please expand acronyms like API
• Please provide a brief description of Doxygen. Why did you decide to use this tool specifically?
• Could you please present the pain points in paragraph format, similar to your key benefits section?
• Near the end you become a bit more casual (“repo”, “lit review”), I’m guessing because you were nearing the end! Would you mind formalizing this a little, for overall consistancy? (also just these casual, wordy sentences at the end: “with little test codes lets you play around with stuff you've already got the next time you're investigating a new …”, etc.)
• Can remove key tools section, if you have none. But I would suggest even mentioning Doxygen here would be safe and smart.

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add (one or more of) the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, as you feel is appropriate. To be honest, I’m not sure what subset of these is correct, since most of your narrative / diagram doesn’t explain exactly what these algorithms you’re developing are used for (data simulation? data cleaning? data analysis? something else?). For adding the appropriate labels, please follow the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please reformat your Diagram to be horizontally (landscape) oriented. Further, your Diagram should occupy no more than 1/2 of a US letter page. This will require reorganizing your boxes.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@chartgerink We need the signed contributor agreement from you, to publish your case study on reproducible research. Please let me know if you see this message, and I'll send information about submitting your agreement. We need it ASAP.

Can you also give me an email address, where I can reach you?

Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. Your Narrative is excellent overall, and we’re requesting the addition of a Title, minor revisions to your Narrative, and re-working your Diagram.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.

Narrative

• For the questions addressed at the end of your Narrative (e.g., “Data: Is your raw data online?”), please remove the questions, and rephrase your responses in the form of stand-alone paragraphs.
• Please read carefully checking for typos or grammatical errors

Diagram

• The text in your diagram is generally too detailed. Please move extra words (e.g., “collect observational data sets”.), and if any detail is totally necessary, it can be moved to your Narrative.
• Text overlapping with sides of some boxes. Please make all text fit within boxes.
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please reformat your Diagram to be horizontally (landscape) oriented. Further, your Diagram should occupy no more than 1/2 of a US letter page. This will require reorganizing your boxes.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution relating to ActivePages very much. The Narrative is extremely well written, but the overall presentation is one level more "abstract" than we're looking for.

Narrative

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail). This can be added at the very beginning of your Narrative, following the example case study linked below.
• Once your Diagram is revised, please update the references in your Narrative to the colored boxes to be consistent your the new black & white Diagram.

Diagram

• Please re-frame your Diagram in the context of your concrete example (molecular dynamics simulations), to clearly relate to the steps described in your Narrative.
• Are you able to consolidate your Diagram into a single flowchart diagram (rather than two)? We realize you're presenting distinct concepts, but this level of abstraction is above what we're looking for.
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and/or “Stage III: Data Analysis” as is most appropriate to your case study, following their definitions in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please provide both the PDF and editable source file for your Diagram.

Here are more traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@chartgerink
Your case study represents a useful and interesting example of reproducibility in applied resaerch using human subjects, and we value this contribution. We’re requesting some minor revisions throughout.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail). This can be added at the very beginning of your case study, following the example below.
• Please provide a little more description of your project in your answer to question 1.

Narrative

• Reading your case study, it’s unclear to me exactly what this project is about. Can you add one paragraph to the beginning of your Narrative, describing the overall project, or the types of projects encompassed by this workflow?
• Please add just a bit to the end of your Narrative, to describing the writing process, and the final steps of your Diagram, and remove the parenthetical statement saying that you’re omitting this.
• Please read carefully checking for typos or grammatical errors

Diagram

• It’s not clear what the right sidebar “Version controlled in Github” is doing there. Either connect it to a box (share results and code in Github?), or simply describe this in your Narrative instead.
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please reformat your Diagram to be horizontally (landscape) oriented. Further, your Diagram should occupy no more than 1/2 of a US letter page. This will require reorganizing your boxes.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Your case study represents a useful and interesting example of reproducibility in neuroimaging data analysis, and we value this contribution. The diagram is very clear. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.

Narrative

• Please read carefully checking for typos or grammatical errors
• The narrative is a little too short, and is intended to be 500-800 words. We suggest to provide more detail on the following:
  • Overall background of your project
  • A little more detail on NeuroVault in the narrative would be very beneficial for the reader
  • Which data preprocessing steps were used?
  • Which data fitting method were used?
  • Elaborate more on the pain points
  • Explain each of the key tools more, perhaps a short paragraph for each

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution relating political science, social media, data sharing and privacy. Your Narrative and Diagram are both excellent, and we're only requesting minor revisions.

Narrative

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail). This can be added at the very beginning of your Narrative, following the example case study linked below.
• Please read carefully checking for typos or grammatical errors (e.g. following sentence “The anonymization was achieved was replacing Twitter and voter unique IDs by randomly generated numeric IDs.”)
• Please define the acronym STAN

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. There's just a small bit of grey, in the outlining shapes. Can you change this to black?
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@garretchristensen
Your case study represents a useful and interesting example of reproducibility in social science research, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.

Narrative

• Typo, should read: “Defense Manpower Data Center” in the introductory questions.
• Could you please remove most of the parenthetical statements from your Narrative? They can either be changed to regular text if they’re important, or removed if not.
• Please read carefully checking for typos or grammatical errors
• Please describe acronym DCVS
• We suggest that you do some rearrangements, e.g., you could move the parts about your concern with the quality of the raw data to the Pain Points section.

Diagram

• Text overlapping with sides of some boxes. Please make all text fit within boxes.
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please reformat your Diagram to be horizontally (landscape) oriented. Further, your Diagram should occupy no more than 1/2 of a US letter page. This will require reorganizing your boxes.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@kallisons Can you please make one minor change (addition) to your case study? Can you elaborate slightly, with just a few sentences in the "Pain Points" section, where the text currently reads:

Archiving my code takes additional time.

Thank you!

We should probably have headers at the top of the three main regions of this diagram.

@poldrack
Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a little more description of your case study in your answer to question 1 in the introduction.

Narrative

• Please read carefully checking for typos or grammatical errors.
• Please explain Connectome Workbench when you first introduce it.
• Can you split the second-to-last paragraph into several, more descriptive paragraphs? This currently seems to include the bulk of the description of your diagram.
• Please rephrase your pain points and key benefits in paragraph style, rather than bullet points.
• Should the non-reproducible pre-processing step be included as a pain point?

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Text is overlapping with sides of some boxes. Please make all text fit within boxes.
• Some of the lines should be straight (e.g.,run_everything -> compare VM results, and also in the top-left of digram, and any others).
• Can you tidy the layout of your boxes, somewhat? It seems more boxes could be “aligned” horizontally or vertically, to improve the visual experience. (ex. the three right-most boxes, the vetical spacing of the three boxes in the lower-left, the size of the two cylinders, etc.
• Please add the label “Stage III: Data Analysis” to your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@yocheah

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a little more description of your case study in your answer to question 1 in the introduction.

Narrative

• Please read carefully checking for typos or grammatical errors
• Please elaborate following “JIRA, an issue tracking system” (i.e., in your diagram you also mention the bug reporting feature that you could mention in your narrative). (Why is a tracking system important?)
• Similarly, please give further information about code building here: “Jenkins, a build system is also used to automate the code build.” (Why is this necessary, why did you choose Jenkins as the tool?)

Pain Points

• Is the following sentence a pain-point? "Since this is ongoing work, we are working on encouraging the use of JIRA as part of keeping track of feature requests and use cases. The use of test procedures are also developed to keep track of the procedures needed to test and to build a full test-suite to help keep track of potential issues.”
  It doesn’t sound like when reading but maybe we are missing something. Please elaborate.

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Hi @chartgerink, we got further revisions some points came up from one of the reviewers:

• The Workflow is very general; it doesn't tell much about the specific project. It would be more interesting and engaging if you included specific details of the research - e.g. what does the data look like? What kind of analyses did you run?
  You mention these in the first paragraph when you introduce the problem but afterwards only describe the workflow in a high level. We would like to see a little more specifics.
• It would be helpful if you could write in past tense instead of future/present throughout the description of your project. The Workflow section is sometimes hard to follow because of this.
• Please describe the acronym OSF the first time you use it in the case study.

@valentina-s
Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a little more description of your case study in your answer to question 1 in the introduction.

Narrative

• Please read carefully checking for typos or grammatical errors
• Instead of saying “I will describe the workflow of a project I did in grad school”, please introduce and explain what the actual project is! I’m sure it will be of interest to readers.
• When you say “most of the research time is spent at this stage”, please give some idea of how much time; days? weeks? Months?
• Maybe consider adding the section on Key Benefits (which was optional), to explain how the field of mathematics is generally conducive to reproducible research, and why?

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• You might consider moving additional details (extra text) from the Diagram to the Narrative.
• Please add the labels “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@kram

Your case study represents a useful and interesting example of reproducibility, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please define “green up”

Narrative

• Please read carefully checking for typos or grammatical errors. There are grammatical errors, sometimes missing words etc. in the current form of the text.
• Please revise and clarify the following sentence: “Close collaborators, and unwitting Twitter followers weigh in during this time.”
• Please briefly describe Zenodo, Figshare, Pandoc when you mention these tools in the text.
• Please briefly describe in which context you use the the tools that you mention (e.g. awk, sed, make file). Also, briefly describe these tools.
• Please expand acronyms like DOI, HPC, API
• Please briefly describe what “(git)ignore” means
• Please change “dois” to DOIs in the last sentence of your narrative.
• There is no mention of the following tools in the narrative (but in the Key tools section) “crossref, Mendeley”. Please briefly describe in which step you use these tools.

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please adjust the arrows in the diagram such that they are straight (e.g., R -> Data Acquisition Script, and statistical analyses -> data viz, and exploratory queries -> scratch githug). The curved arrows make the diagram look unnecessarily busy.
• Please change “scratch github” to “scratch github repository” for consistency with the narrative.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. We’re requesting the addition of a Title, increased detail in your Narrative, and minor revisions to your Diagram.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.

Narrative

• Please read carefully checking for typos or grammatical errors
• Please introduce and explain Gush, PlanetLab
• Could you please expand your Narrative to the suggested length of 500-800 words? In particular, the 3rd and 4th paragraphs seem to very briefly cover a huge amount of material. I would suggest expanding these significantly, to slowly provide a one-to-one description of the boxes in your Diagram. This will make the entire case study more clear.

Diagram

• Might consider vertically aligning the three left-most boxes.
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@kallisons
Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. For your case study, were looking for only one Diagram and one Narrative. Can you please reformat in this way? The style and presentation of kasmislan_researchworkflow.pdf is what we’re looking for. We’re also requesting the addition of a Title, and some minor revisions to your Narrative. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a little more description of your case study in your answer to question 1.

Narrative

• Please combine into one Narrative outlining your reproducible workflow.
• Please read carefully checking for typos or grammatical errors.
• Rather than “In this narrative”, please say “In this case study”.
• Please introduce and explain D3 in your narrative.
• Please describe what netCDF fileformat is and which fields

Diagram

• Please combine into one Diagram showing your reproducible workflow. Please follow the style of kasmislan_researchworkflow.pdf.
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Your case study represents a useful and interesting example of reproducibility in applied scientific research. However, in its current state, both the Narrative and Diagram will require significant revision. We’d like to receive revised case studies no later than April 8th.

Narrative

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail). This can be added at the very beginning of your Narrative, following the example case study linked below.
• Your Narrative appears to be in outline format. Please reformat as prose, in the form of complete sentences and paragraphs.
• Your Narrative includes assignments to individuals (e.g., (J. Millman, P. Stark)). We don't see how these relate to your case study; unless they are somehow necessary, please remove them.
• Your Narrative includes time requirements (e.g., Time: approximately 4 hours). We don't see how these relate to your case study; if you decide to keep these, then please explain them clearly in your Narrative.

Diagram

• Please reformat your Diagram to be horizontally (landscape) oriented. Further, your Diagram should occupy no more than 1/2 of a US letter page. This will require reorganizing your boxes.
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis”, following their definitions in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change the grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please provide both the PDF and editable source file for your Diagram. For the editable source, please use a graphical flowchart editing tool such as draw.io.

Here are more traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Tara,
Your case study represents a useful and interesting example of reproducibility in the field of neuroscience, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a little more description of your case study in your answer to question 1 in the introduction.

Narrative

• Please read carefully checking for typos or grammatical errors.
• Please expand acronyms like fMRI, MNI (what is MNI please describe briefly) when you use them the first time.
• Can your narrative be made to more closely align with the workflows shown in your diagram?
• Please add citation for the Time curves paper.
• The paragraph beginning “Preparation of data for functional….” seems overly technical. Is there any way you could explain some of the tools used here better, in terms of what they actually accomplish, and how they’re reproducible? This might require splitting this paragraph into multiple paragraphs. Also please describe the acronyms here too.
• Please be consistent in word capitalization when you refer to tools (e.g. meica.py vs. MEICA vs. ME-ICA (in the diagram)).
• You have a good explanation of Make in the Key Tools section. We would suggest to move this to the narrative where you first introduce Make.

Diagram

• Please remove the big box at the top “Rest State Preprocessing Pipeline”
• Please make the arrows to be narrow black lines (as in our sample diagram, below).
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please reformat your Diagram to be horizontally (landscape) oriented. Further, your Diagram should occupy no more than 1/2 of a US letter page. This will require reorganizing your boxes.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@aaarendt We received a signed contributor agreement from Christian Kienholz, referencing your case study.

Should be be listed as a co-author on your case study? Just let me know, and I can add him on.

@zhaozhang

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a little more description of SEP library (either here or in the narrative)

Narrative

• Please briefly describe Spark. Why did you decide to use Spark?
• Please briefly describe what FITS images are.
• In the following sentence: “4. Thread safety, neither the jFITS library nor the SEP library is thread safe” . Please briefly describe what you mean by thread safe.
• We suggest to take the following sentence out. “ I was in charge of the coding, and Kyle, Frank, and Evan provide technical advise.” Please provide full names if you choose to keep it.
• Please briefly describe and elaborate why you choose to use NERSC and EC2 S3. Please describe what these systems are.
• Please describe the acronym JVM

Diagram

• We would suggest making the overall “flow of information” to be more clear in your diagram. This might involve (1) removing or combining some boxes, or (2) removing some of the arrows, to simplify your diagram, and make the overall workflow more clear. For example, where does the main flow of information start, and where does it end?
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please keep your Diagram to be horizontally (landscape) oriented, buy occupying closer to 1/2 of a US letter page. This may require reorganizing your boxes, or removing some amount of detail from your diagram.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

• Is there a public link to the database, or the Shiny app that you've created?

• If there is no suggestion for the last question (Would you recommend any specific websites, training courses, or books for learning more about reproducibility?) then delete entirely.

I'm guessing no. I sent something around on Slack with no response. If it is still in progress, I finally have something I'd like to submit.

@mesnardo
Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a short (1-2 sentences) description of your case study in your answer to question 1 in the introduction.

Narrative

• Please shorten your case study to have 500-800 words. Right now, your case study has 1639 words, which we believe is too detailed and can be shortened. We are looking for a brief description of your study with the important computational workflow, presented in a simple and basic manner, such that someone outside your field can follow the basic steps. Your diagram is very clear and has the information we are looking for but your narrative gets lost in details sometimes.
• Please read carefully checking for typos or grammatical errors
• Please add (Barba, 2012) in the references
• Please briefly describe “figshare, CC-BY” the first time you use in the text
• Please define acronyms such as CFD (move from Introduction to Narrative), GPU,
• Although we realize that a more detailed description about Krishnan et al. 2014 comes in the second paragraph in your narrative move the description about this study from the Introduction to the Narrative. In general, you could move some information from the Introduction to the Narrative. In the Introduction we are looking for a shorter 1-2 sentence description of your case study.
• Please briefly elaborate any specific reason to use the CUSP library. Such information can be very helpful for the interested reader.
• Is “IcoFOAM” part of “OpenFOAM” please state so if yes. This information is missing.
• Please briefly explain the term “vorticity”, to help readers to follow your case study without prior knowledge.

Diagram

(The diagram is very clear and comprehensive we only request minor formatting.)

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please reformat your Diagram to be horizontally (landscape) oriented. Further, your Diagram should occupy no more than 1/2 of a US letter page. This will require reorganizing your boxes.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Additional case study from dsinghania will need an image in pdf format rather than png.

I'm having some problems with using Command Line Tools with AWS and MTurk. I have followed these instructions: https://requester.mturk.com/developer/tools/clt and then followed the 'Get Started' instructions - and Command Line finds 'bin' in the AWS folder, but can't run any commands. It simply returns a 'cannot find path' message. We've even made sure we have the exact version of JAVA mentioned in the script (5.0.6). Is there anything you can suggest? We're at a bit of a loss here!

Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. Overall it’s excellent, and we’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.

Narrative

• Please read carefully checking for typos or grammatical errors.
• You only briefly mention Overleaf in the key tools section. If this is truly a key tool, then please add the usage of it to your Narrative (possibly also in the relevant spot of your Diagram), and explain it’s usage and importance in some detail.

Diagram

• Please remove the little semi-circles in the lines, where they overlap. Not necessary, it’s understandable where the lines are going.
• Please make it so the lines from the top-left box (Sources) don’t cross.
• Please adjust the lines surrounding the central box (Software Tools) so they don’t go behind (in the top left) or over (in the lower right) the central box.
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution relating to Docker and Open Lab notebooks very much. We're requesting some revisions for your Narrative, and a re-design of your Diagram to a more standardized presentation.

Introduction:

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail). This can be added at the very beginning of your Narrative, following the example case study linked below.
• Please elaborate your project and the general motivation and purpose substantially more. This should really motivate what your case study is all about.

Narrative:

• Please explain the OpenLab Notebook concept better in the beginning.
• Make sure terms like ruby, jeykll, .Rmd files, knitr, DockerHub, Dockerfile, continuous integration, unit testing, Roxygen, are introduced and described.
• The narrative should be a step by step walk through of your diagram with additional information. This link is currently not very clear. One suggestion would to number the different steps in the narrative as well as diagram (e.g. 1. Explore new ideas in open lab notebook, 2. Create public GitHub repository for project, using an R package layout, etc.)
• Please elaborate the following paragraph starting with “Notebook pages do not load these functions as a single package ….”

Other Sections:

Did you mean to leave the following sections blank? Would be great if you could add your experience, as we really think these sections are very beneficial to the reader.

• Pain Points. Can you add something here?
• Key Benefits. It seems you have a lot of benefits you could describe!
• Key Tools. Likewise, it seems you have a lot of key tools that you could mention.

Diagram:

• Please make all lines straight, or using right angles.
• Please do some alignment within the diagram. e.g. “Infrastructure View” and “Elements View”, and also align the two “Zenodo archive DOI” boxes, etc.
• Please ensure that all lines don't overlap with text.
• Odd hyphenation for “version-ed”. Please fit this word on a single line.
• Generally tidy, clean up, and make more consistent & presentable, generally following the format of the example Diagram linked below.
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the label “Stage II: Data Processing” to your Diagram, following the examples in CaseStudies123.png as a guideline. This label should be in Helvetica font, bold, 22pt.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please provide both the PDF and editable source file for your Diagram.

Here are more traditional examples of a case study Narrative and Diagram, which represent the style (in particular for the Diagram) that we're looking for.

Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. The narrative and diagram are overall very clear, however, we're requesting some minor revisions.

Introduction

• Please elaborate your project and the general motivation and purpose substantially more. This should really motivate what your case study is all about.

Narrative

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail). This can be added at the very beginning of your Narrative, following the example case study linked below.
• Please read carefully checking for typos or grammatical errors
• Define acronyms like CBD
• Briefly describe terms like csv-file, SPSS, IDE
• Please update paper information if published (“An initial paper reporting the results is currently under review.”)
• Ideally, your narrative is a step by step description of your diagram with additional information. Although the diagram is neat, the link to the narrative is sometimes missing. We strongly suggest you to use the same words in the narrative as well as the diagram (e.g. where is codeDir represented in the diagram? Is that information in a user specific config file?)

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might still use different shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools. We didn’t understand the use of the half color (or grey) and half white boxes.
• We suggest you to label the different repositories that you mention in the narrative in your diagram.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@jgukelberger
Your case study represents a useful and interesting example of reproducibility in applied computational physics, is very well-written. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a little more description of your project in your answer to question 1.

Narrative

• Please read carefully checking for typos or grammatical errors
• Please explain VisTrails, at least briefly, when you introduce it.
• Feel free to add a markdown link to your publication, if you want to.
• Mixed capitalization between vt and VT, please make consistent (in the context of vt workflows)
• Mixed capitalization between alps and ALPS, please make consistent
• We would suggest making your side remark in [ ] to be normal text.

Diagram

• Typo in your diagram: provenanve?
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@choldgraf Can you please add a short description of PEP8 and PEP257 checkers to your case study, for those who are unfamiliar?

Please make sure to submit changes to the submissions branch.

Thanks!

@jkitzes: I added two new references (included both bibtex and APA form at the end of the case study) to my own case study. How shall we proceed on updating the references. I know that you did this last time, so let me know what is your preferred way to do this.

also I actually pushed these changes already w/o a PR. I thought I was operating on my fork but wasn't. lmk if that is fine.

Your case study represents a useful and interesting example of reproducibility in applied political science, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.

Narrative

• Please read carefully checking for typos or grammatical errors
• Please carefully run a spell-checker on your Narrative. “re elected”, “foreing”, “foregin”, “ny”, “Softwarer”, “muste”, “dta”, “shoild”, etc.
• Please briefly define jargons like “data scraping, scraping the website”
• Please define the acronyms used in the narrative (e.g. GUI)
• Please provide more detail about the tools, inputs, outputs, and reproducible strengths in points b2, b3, b4, and b5. These are all excellent examples that you give, and it would be helpful to have you explain them even more. This section will be extremely useful for readers.
• The same goes for your Pain Points, Key Benefits, and Key Tools. These are all good information. Please feel free to expand them, or just explain a little more, if you can.

Diagram

• We suggest to label the steps in your diagram with the labels you used to describe your narrative (a1, a2, etc.)
• Please carefully look at the more traditional example of a Diagram (link below), and revise your Diagram to generally follow this format.
• Remove all the icons. Replace them with text boxes (“Python”, “Zotero”, “LaTeX”, etc).
• Make the arrow that is pointing from “research plan” towards python actually point to Python.
• Please make the arrow pointing upwards towards RStudio to be straight.
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represents the style we're looking for.

Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. We're requesting some minor revisions in your Narrative and Diagram.

Narrative:

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail). This can be added at the very beginning of your Narrative, following the example case study linked below.
• Make sure that GIS, LiDAP, PostGIS, SQL, PostgreSQL, ArcGIS, SQLAlechmey, are introduced and described with one or two sentences.
• Please add a few sentences for the importance of the choice for Microsoft Azure (or in general clouds) and RDBs. This information could be very useful for someone who wants to use this workflow as an example for a similar problem (e.g. in another domain).
• It’s unclear that detailing the contributions of individuals is necessary or important in your Narrative (e.g., E. Burgess generated the majority of the Python code to build plots…, etc). We suggest removing this level of individual contribution, unless there is a good reason otherwise.

Diagram:

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• You may need to remove extra details from your Diagram (and put them in the narrative) to be able to achieve the minimum size font.
• Remove all icons from your Diagram. Replace them with text boxes (“Python”, “MS Azure”, etc).
• Boxes in the middle have outlines / grey boxes slightly overlapping or missing, please adjust these.
• Some labels (e.g., Linux Virtual Machine) are overlapping with boxes, or touching sides of boxes, please adjust slightly.
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study: Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Deepak, @dsinghania
I know this has taken us forever, but we'd like to include your case study in an online appendix of our volume. (We didn't get enough submissions to justify a second edition, but the online book looks really good, and the print version is yet to come out. See https://www.practicereproducibleresearch.org/)

I have made some minor grammatical edits. Would you mind making the following edits and then submitting a pull request with the updated version (or email it to me, that works too)?

• update link to Burgess et al. (2014)

• which version of Stata did you use?

• Provide link to WB website under INDO-DAPOER page

• Either add info to key tools section or remove entirely

@kbarbary
Your case study represents a useful and interesting example of reproducibility in cosmology, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a little more description of your case study in your answer to question 1.

Narrative

• Please read carefully checking for typos or grammatical errors
• Please remove [NOTE: Consider putting this intro paragraph before the diagram?]
• Mixed capital letters used for sncosmo, please be consistent (also check the diagram and update if necessary)

Diagram

• Please use same capital letter as in the narrative for sncosmo, i.e., SNCosmo
• Suggestion: Rename “local repository” to “local git repository”
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the label “Stage III: Data Analysis” to your Diagram, following the examples in CaseStudies123.png as a guideline. This label should be in Helvetica font, bold, 22pt.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@katyhuff
Your case study represents a useful and interesting example of reproducibility in nuclear engineering, and we value this contribution. We’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a little more description of your case study in your answer to question 1.

Narrative

• Please briefly define/describe CMake, Nose, Doxygen, Sphinx
• There is information in the diagram that are not mentioned in the narrative (e.g. most right part of the diagram). We suggest that you, at least, add these steps with a little more detail in the “In summary, the research workflow in this framework has the following steps”
• Please read carefully checking for typos or grammatical errors. (e.g. “A discussion of our workflow around these proposals here”)

Diagram

• Some labels (e.g., “Join Filter”, and “Cleaned, Structured”) are overlapping with boxes, or touching sides of boxes, please adjust slightly throughout.
• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the label “Stage I: Data Input” to your Diagram, following the examples in CaseStudies123.png as a guideline. This label should be in Helvetica font, bold, 22pt.
• Please reformat your Diagram to be horizontally (landscape) oriented. Further, your Diagram should occupy no more than 1/2 of a US letter page. This will require reorganizing your boxes.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

@jkitzes
Thanks for still requesting an issue. I’ll prune this down just to the things that are relevant to you, and hence should be revised, so please check out the points below.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a little more description of your case study project, in your answer to question 1 in the introduction.

Narrative

• Consider adding a link to the final publication that you mention at the beginning of your Narrative: “The final analysis was published in PLoS ONE (doi:10.1371/journal.pone.0096341)”
• Can you provide more background and information about BatID, since this is unique to your case study and won’t be explained in the glossary or anywhere else.
• Consider adding Key Tools section (although this is optional)
• Please read carefully checking for typos or grammatical errors

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels “Stage I: Data Input”, “Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.

Hi @pablobarbera, we got further revisions back and one question came up regarding the following sentence in your case study:

"This is information that most users are not aware could not be inferred based only on their public personal information, which raises the question of whether the concept of informed consent in sharing users' data -- as defined in the Terms of Service that users accept when they sign up for a Twitter account -- applies in this context as well."

Did you mean "could be inferred", instead of "could not be inferred"?

I can make the change in your case study once you confirm either way. Thanks!

@jkitzes: The formatted versions of the case studies are now in the submissions_cleaned branch.

fyi, in all case studies, I moved the question

(2) Define what the term "reproducibility" means to you generally and/or in the particular context of your case study.

from the Introduction to the end as a new question with the following headline

What does "reproducibility" mean to you in general and/or in the particular context of your case study?

@rjleveque
Your case study represents a useful and interesting example of reproducibility in applied scientific research, and we value this contribution. It’s extremely well written, and we’re requesting the addition of a Title, and some minor revisions to your Narrative and Diagram. We’d like to receive revised case studies no later than April 8th.

Introduction

• Please provide a one sentence “title” for your case study (e.g., “Developing, testing, and deploying efficient MCMC algorithms for hierarchical models using R”, or an equivalent level of detail), at the very beginning of your case study, following the example below.
• Please provide a little more description of your case study in your answer to question 1 in the introduction.

Narrative

• Please read carefully checking for typos or grammatical errors.
• Please expand UW, FEMA, at least the first time you introduce it.
• Please explain rsync, when you introduce it.
• More explanation regarding your choices to use git, but not github, and the rationale behind not version-controlling the datasets might be useful.
• I feel more comments about the BitBucket decision would be useful. Why was it used? Was this an advantage, or a nuissance? I feel the use of both git and bitbucket should either be listed as a pain point, or a key benefit.

Diagram

• Please make the minimum font size in your diagram to be 10pt, and more ideally 11pt (space allowing), using Helvetica font (or similar).
• Please add the labels Stage II: Data Processing” and “Stage III: Data Analysis” to indicate the appropriate sections of your Diagram, following the examples in CaseStudies123.png as a guideline. These labels should be in Helvetica font, bold, 22pt.
• Please change any color/grayscale in your diagram to black & white. You might consider using additional shaped boxes, or various outline styles for boxes (and adding a legend) to denote different types of information or tools.
• Please keep your Diagram horizontally (landscape) oriented, and occupying no more than 1/2 of a US letter page.
• Please provide both the PDF and editable source file for your Diagram.

Here is a traditional examples of a case study Narrative and Diagram, which represent both the style and degree of "concreteness" that we're looking for.