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Maintaining a journal

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Table of Contents

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Some examples of LabBooks provided for inspiration

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+Since a few years, we systematically require any or our students to +have a laboratory notebook in org-mode. Most of the time, they start +in private repositories but often end up being fully opened. Here are +a few ones: +

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  • Luka Stanisic (a former PhD student advised by Arnaud Legrand) starting +using this methodology during his Msc and developed further +throughout his PhD. Part of his PhD thesis was actually about +designing a methodology for reproducible experiments in large scale +distributed systems. You may want to have a look at his postdoc +LabBook and to the report of Léo Villeveygoux whom he advised.
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  • Tom Cornebize is currently a PhD student advised by Arnaud Legrand +and during his MSc, he also heavily loged his activity on Github.
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  • Lucas Schnorr's students usually also maintain their journal in a +very nice way: Tais Bellini's BSc., Arthur Krause’s LabBook
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  • Martin Quinson's students also follow such conventions: +
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    • Ezequiel Torti Lopez, M2R 2014. Report, with both the data provenance and the data analysis included in appendix.
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    • Betsegaw Lemma, M2R 2017. LabBook
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    • Gabriel Corona, engineer on SimGrid, 2015-2016. Journal, Blog (findings).
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    • Matthieu Nicolas, engineer on PLM, 2014-2016, Journal.
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+Org-mode is obviously not the only option and many of our students use +am mixture of org-mode, rstudio and jupyter depending on what is more +convenient. +

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How to report efficiently (by Martin Quinson)

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+My friend Martin has gathered an excellent compendium of information +and references on his webpage to explain his students what he expects +from them. I'll therefore simply paraphrase him here with the most +important aspects related to reporting but feel free to read the +original version: +

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Reporting

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+I ask you to write a little reporting regularly. Depending on the +situation, it may be every day, every week or every month. In any +case, your reporting is very important for the following reasons: +

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  • It forces you to think about what you are doing, which may help you +to unblock your problem by your own. Writing down the problems in a +clear way is often sufficient to see the solution appearing.
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  • It helps me following your progress even between the meetings. I +cannot unblock you if I don't detect that you are on a wrong lead or +otherwise blocked.
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  • It keeps a track of the steps in your work. That's good for the day +where you want to write your final report (even if a final report +should never be presented in the chronological order). That's good +for the next after you who will be supposed to continue you effort, +or to build upon it.
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  • That person may be yourself (if you go for a PhD program), another +intern, myself or even someone else on the Internet: that's what we +call Open Science, an effort where everyone can build upon the +scientific work of everyone.
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+I want you to write your reporting in an org file (yep, you don't have +a choice here). [..] +

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Reporting Logistics

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+Once you're setup with all software installed and somehow configured, +you need to create a reporting file in a place where I can see it and +where it won't get lost if your disk crashes or something. Open a +dedicated git repository (on github, gitorious, gitlab, …) for +that. After your internship, your report should be archived directly +in the source tree of the software that you are working on, if +any. But having your reporting located in the source tree may +complicate things during your work. +

+ +

+Yes, it means that your file will be public at some point, but that's +why we call it "Open Science", after all. Also, you should write it in +English if possible. The part of your reporting that is called +"Journal" (see below) may be written in French if you are more +efficient this way but the rest must be in English. Don't make your +tone too formal because the file is public. Make it efficient. Nobody +will ever blame you for the work you did during an internship a long +time ago. If you really want, we can even make this file +anonymous. Just speak to me. +

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+You want to write your reporting before leaving work. Weekly reporting +should be written on Friday, one or two hours before leaving. That's +the best solution to have a nice week end without thinking about work, +and still lose no information that you would need on Monday morning. +

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Reporting Document Organization

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+Your reporting document should have four main parts: +

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Findings
This section summarizes the general information that you +gathered during your work. It is empty at the beginning +of your internship, and gets fleshed with the important +things that you find on your way. That's where +bibliographical information go, for example. But that's +definitely not where TODO notes go (see below).
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Development
This section presents the technical sides of your +work. Don't write anything in there yet. Put it all +in the Journal part for now.
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Journal
Describe the day-to-day work done for each period (day, +week or month) of your internship. That's the most +important part of your reporting, and we come back to it +below.
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Conclusion

+That's what you write in the next week of your +internship. You can see it as a letter to the next +guy, explaining the current state of your work, a few +words about its technical organization, and what +should be done next on that topic. Keep this part +highly technical, the overall organization of your +internship will be seen in your final report. +

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+The Journal part is the only part that you may write +in French on need. You want to add one subsection per +period to your journal. Don't make it too long, or you +would waste time writing long texts that very few will +ever read. Don't make it too short or it will be +impossible to understand it on Monday morning (or +three months after). Finding the good balance is +sometimes difficult, but I will provide feedback on +your first entries, so don't worry. +

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+Each of section describing a period should contain three subsubsections: +

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Things done
a few words about what you've done. Something like 2 +or 4 items with a few words describing what you've +done. You can omit the title of that section and put +the items directly in the upper section (see the +example below).
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Blocking points and questions
try to explain clearly the things +that block you or slow you down. If you found the solution +already, then it should be part of the previous subsection (but +you should say a few words nevertheless). Also ask every question +that you may have for me in that section. If the question are +personal (e.g., about the logistics of your internship such as +salary or so), please prefer emails that are not publicly +visible. If this section is empty for a given period, skip it +all together (no empty subsubsections).
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Planned work
A few items about what you plan to work on during +the next period.
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+A template of reporting file is given at the end of this section. This +is just a strong advice: If you really feel better with another file +organization, then give it a try for one period, and ask for my +feedback. I can adapt, and I do not pretend that my advice is the +definitive answer. It's just the result of my experience so far. +

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+Notice how TODO items are written: they are given as items in the +Planned work sections of the journal. As explained in the +documentation, you simply have to write "[ ]" in front of items that +you plan to do in the future. +

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+You should add a [1/] on the "Planned work" line, so that emacs keeps +track of what is done and what is still to do. Once they are done, you +type C-c C-C on their lines to change the blank box [ ] into a checked +box [X]. Also, the [1/] will be changed to denote the amount of work +that is still to be done. +

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+At any point, you can see all ongoing TODO items with the following +keystrokes: "C-c / t". More information on TODOs in orgmode's +documentation. The important thing here is that most TODO items must +only be written in the Journal part (so that we know when they +occured). +

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+Do not edit past entries of your journal, unless you have very good +reasons. If you must, make sure that you don't lose information about +the path that you took (remember the Open Science thingy). You should +always add information to past entries, such as: +

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- *edit* This hypothesis does not hold; see the entry of [the day where you found it] for more information.
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+The only exception are TODO entries, that should clearly be rewritten +to DONE entries. If you need to adapt your TODO entry (because the +initial goal was poorly stated or otherwise), change the initial entry +from TODO to CANCELED (or check the box after stating in a subitem +that it was not done but canceled, and why), and create a new TODO +entry in the current period section. +

+
+* Introduction
+This file contains the reporting for my beloved internship done on
+this topic on that year. For now, just add the official title of
+your internship (check the convention signed between your
+university and my lab). After a few weeks, once you really
+understand your internship, you should write a few paragraphs about
+the context, problem and motivation of your work, with some
+possible use cases. But don't do that right now.
+* Bibliography
+* Journal
+** Week 2 feb
+- read the doc about writing my reporting
+*** Questions
+- do I really have to use emacs?
+*** Work Planed [1/2]
+- [X] install emacs and setup orgmode
+- [ ] read the provided articles
+** Week 9 feb
+- Installed emacs    
+(omit the Questions section if no question)
+*** Work Planed
+- do some useful work
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