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2020-04-18Edits in the text to make it shorter and fix a few mistakesMohammad Akhlaghi-20/+14
A few minor issues were found and fixed in the text. I also tried to shorten it a little further.
2020-04-17Minor typo correctionsMohammad Akhlaghi-3/+3
I forgot to put these in the last commit! They are now implemented.
2020-04-17Edited the text, normal sized bibliography and TARGETS.conf in figMohammad Akhlaghi-67/+71
I had another look at the text and tried to summarize it a little more while also fixing several typos that I had just discovered! In the process, I noticed that we hadn't actually put a link to Maneage's main Git repository! So we now have the URL as a `git clone' command. Also, I thought that its better to show the `TARGETS.conf' file (which we actually talk about) in the file architecture instead of `LOCAL.conf.in' (which we don't talk about any more!). Finally, to be more similar with DSJ, the bibliography is now in normal font size, not footnotesize.
2020-04-15A single word correctionMohammad Akhlaghi-1/+1
In the introduction I had mistakenly put "metadata" instead of "workflow", its corrected with this commit.
2020-04-15Acknowledged Ryan O'Connor (from RDA), for his commentsMohammad Akhlaghi-1/+1
Ryan O'Connor is from RDA and my principle contact for the grant. He also kindly went over the first draft of the paper and gave useful and encouraging comments.
2020-04-15Commented the note to DSJ editors and refereesMohammad Akhlaghi-2/+2
This was only relevant for the submitted version, so I am committing it until the next submission.
2020-04-15Minor typo correctionsMohammad Akhlaghi-12/+11
After the submission and reading through the text another time I found some typo corrections and fixed them. Also now that David is an author, I removed him from the people to acknowledge (David brought this up himself, thanks David ;-)).
2020-04-14Added note with link to paper's distribution tarballMohammad Akhlaghi-0/+3
Since the journal doesn't accept supplementary files during initial submission, I have put this link on the PDF for the referee and editors to access if they want. Also the `tex/img' file was added to the distribution tarball.
2020-04-14Imported David's corrections into the main paperMohammad Akhlaghi-202/+213
Thanks David ;-)! I tried to implement as many as I could. For the time being, I just removed teh `~' between "Section" and its number, and removed the italics on software names. Let's see what the journal editors say about it. Otherwise, most of the suggestions were very good and indeed made the text much better to read.
2020-04-14Some corrections to help make the text more clearDavid Valls-Gabaud-261/+261
David submitted these comments by email, I (Mohammad) am committing it into the project.
2020-04-14Further text shrink, added Competing interest and Author contributionsMohammad Akhlaghi-68/+91
To make the text easier to read and further comply with the author guideline, the text was shrank a little more and the two final sections were also added on "Competing interest" and "Author contributions". I also found the CODATA logo on Wikipedia in SVG format (vector graphics), so I replaced the previous pixelated PNG format with the PDF (converted from SVG).
2020-04-14Addressed points raised by Raul in previous commitMohammad Akhlaghi-5/+2
I removed the part emphasizing one journal, but about the comment at the end of the conclusion (to say some negative things): we have already done that in the discussion, mentioning the caveats ;-). But you are right, we should summarize the caveats is well.
2020-04-14Minor typos fixed up to Section 6: DiscussionRaul Infante-Sainz-21/+22
With this commit, minor typos have been fixed from Section 4 to 6. The majority of them are minor corrections (typos/spelling). I added just a couple of comments/suggestions in red. If you think they are necessary try to fit with the latest modifications. If not, just ignore them. Really nice paper, congratulations to all contributors!!
2020-04-14Minor typos fixed up to Section 3: PrinciplesRaul Infante-Sainz-16/+17
With this commit, just minor typos have been fixed (I am rushing over the text since we are out of time!). There are also a suggestion in order to remove a couple of phrases to try to be more aseptic when comparing with another project. But there is only an idea, take it or not as you consider.
2020-04-14Added first summarized draft of discussion and conclusionsMohammad Akhlaghi-16/+31
A first draft for these was added and will probably become much better in the next few iterations.
2020-04-14Edited/shortened the main body, first draft of summarized discussionMohammad Akhlaghi-267/+188
I went through the whole paper and tried to decrease its size even futher, also a first draft of the summarized discussion has been added.
2020-04-13Installation year removed from TeXLive installationMohammad Akhlaghi-9/+10
TeXLive recently transitioned from its 2019 version to its 2020 version thanks to Elham Saremi's trial of the this project. The fact that traditionally Maneage installs all TeXLive packages in a per-year directory is very annoying and required an update in the core Maneage system every year. So I suddently recognized that we can fix this by setting a different name for the directory holding the release year. This has been implemented with this commit. I have also done this change in the main Maneage branch for other projects to also benefit from this correction.
2020-04-13Implemented Roberto's raised points in the paper's sourceMohammad Akhlaghi-24/+20
Thanks Roberto, they are now implemented.
2020-04-13Minor corrections and thoughtsRoberto Baena Gallé-99/+101
I corrected bugs, typos, double words, and punctuations along the whole text. I do some comments which are always highlighted with \hl{this is my comment}, so you can identify them easily in the pdf. If you want to remove, then you can do it easily with Ctrl+R since I think you never used \hl. Finally, I added my name as coauthor but, please, feel free to remove it if you want. Note from Mohammad: since there were two other suggested commits before this that were already merged, I rembased Roberto's commits and fixed a few minor conflicts.
2020-04-13Imported Pedram's corrections, no conflictsMohammad Akhlaghi-8/+8
There weren't any conflicts in this merge.
2020-04-13Added short line to inform that there are tutorialsRaul Infante-Sainz-0/+1
With this commit, a short line telling that Maneage has tutorials showing the workflow in a practical way has been added. Because of we are near to the limit of words, I have added just a very short line. The sentence does not specify any file name since the tutorial(s) is not included (it will be in a near future).
2020-04-13Adding Julia to acknowledgments for creating the logoRaul Infante-Sainz-0/+1
With this commit, I have included a small line to recognize Julia Aguilar-Cabello as the designer of the Maneage's logo.
2020-04-13Fix typosPedram Ashofteh Ardakani-8/+8
2020-04-13Full existing contents summaried, only discussion to goMohammad Akhlaghi-32/+449
The contents until two commits ago when I started to summarize the paper are now in a new and shorter format: previously the discussion started on page 25, but now it starts on page 17. It is still a little longer than 8000 words, but not as significantly as before. I will add the discussion and also try to summarize it futher before submission.
2020-04-12First draft of first three sections of shortened paper are doneMohammad Akhlaghi-0/+418
As described in the previous commit, we had to shorten the paper to roughly 8000 words (which is significant decrease!). With this commit, I am committing the current version of the summarized paper, where the introduction, defintions and principles have now been summarized. I am now summarizing the rest (describing Maneage and the discussion).
2020-04-10Renamed initial paper to paper-long.tex, to write shorter new versionMohammad Akhlaghi-2588/+0
We just recently recognied that the final paper should not be longer than 8000 words. The easiest way was just to start a new `paper.tex' and bring in parts from the original/long version. We can use all the hard work that went into writing the long paper later (possibly in a manual for Maneage). So I don't want to suddenly distroy its history at this point. To let Git know about renaming the original `paper.tex' to `tex/src/paper-long.tex', I am making this commit. This commit doesn't have any `paper.tex' and only records the fact that it has been renamed. In the next commit, I'll re-create `paper.tex' which will host the short/final version. But thanks to this commit, if we later make any changes to long version, Git will know that it was originally the main `paper.tex'.
2020-04-10Acknowledged the help of Pedram, Zahra and SurenaMohammad Akhlaghi-0/+1
Thank you very much guys :-).
2020-04-10Fix spelling errors, suggest alternative wordsPedram Ashofteh Ardakani-135/+135
I tried to get all the words I knew. Some may be correct in different conventions. It definitely needs a second or third review for spell checking. Suggested some additional formatting, including but not limited to using the LaTeX \textsuperscript{} command for stating dates. Also, some unfamiliar rare words that finished with `-able` or `-ability` may need to be changed. Finding better alternatives to better simplify and ease the `readabiliy` ;-) of the paper - I see it's hard not to use them actually. It has got me wondering what better alternatives are available? We'll find out.
2020-04-10Suggest minor changes in the abstractPedram Ashofteh Ardakani-8/+9
to shorten some sentences, fix some spelling/typos, and further simplify some parts. I can see that there are some spelling errors in the rest of the paper. They will be taken care of in the next commit.
2020-04-10Imported Raul's corrections to the paper, minor conflict fixedMohammad Akhlaghi-50/+55
There was only a small conflict in the abstract with Zahra's corrections and that has been fixed.
2020-04-10Minor corrections based on Zahra's suggestionsMohammad Akhlaghi-7/+9
A parenthesis was added to the abstract to hightlight the importance of data lineage for reproducibility. Also, the definitions that Zahra had given for reproducibility were added as comments above the part on defining reproducibility. We'll later decide how to blend them in, if possible.
2020-04-09Minor typos and spelling corrections in Definitions, some notes addedRaul Infante-Sainz-24/+25
With this commit, I have corrected several minor typos in Section 2 (Definitions). I have also put a couple of notes for modify or ignore some phrases.
2020-04-09Minor typos and spelling corrections in IntroductionRaul Infante-Sainz-17/+17
With this commit, minor typos have been corrected in the Introduction section. The majority of them are just small corrections, others are in order to not use contractions ("did not" instead of "didn't" and so on). Other modifications have been added with the aim of remove some small portion of the phrases to make it more focused.
2020-04-09Trying to make the Abstract shorter, keywords sorted alphabeticallyRaul Infante-Sainz-11/+9
With this commit, I have tried to make the Abstract a bit shorter. I think it was too long considering that there are plenty of space in the paper to describe some of the points that were noticed in the abstract. The main point is just to try to be atractive to the reader being focused to the main points. In any case I think there are room for improving it. The keywords have also been sorted alphabetically.
2020-04-09Adding Raul as co-author of the paperRaul Infante-Sainz-1/+2
With this commit, I have added my name as co-author of the paper. Since my affiliation is the same as Mohammad's affiliations, I did not have to add any additional line for that.
2020-04-08Reproducibility in the abstractzahra sharbaf-2/+7
Because one of the most important properties of Manaege is reproducibility. I think is it better to say something about it in the abstract, like the thing that you do in your speech. With this commit, I noted something about it in the abstract.
2020-04-02Rewrote abstract, better organization in publishing sectionMohammad Akhlaghi-26/+116
I hadn't updated the abstract since first writing it. With this commit, it has been updated to be more precise and generically interesting, focusing more on the principles and usability. I also greatly improved the section on publishing the workflow.
2020-04-01Completed first draft of group working in build directoryMohammad Akhlaghi-4/+21
This section (of sharing a build directory between multiple members of the project) is also a good features of Maneage.
2020-03-31First draft of the version control section and figure completeMohammad Akhlaghi-22/+38
The figure was greatly improved, becoming much more clear and descriptive of some of the main advantages of having version control in a complete project like Maneage.
2020-03-30Section on starting new projects, and publishing project addedMohammad Akhlaghi-14/+77
With the main structure of Maneage explained, I have started to explain how a new project is created, along with a schematic diagram that shows two scenarios of how Git can help with project management.
2020-03-28Cleaned up the introduction, definitions for provenance and lineageMohammad Akhlaghi-117/+184
Until now, the introduction had repeated several things and also had a relatively long list of things to add in its end. Also, it was highly focused to scientific papers. With this commit, I effectively re-wrote it, with the starting paragraphs becoming more industry-friendly, while also focusing on the scientific cases. Many of the repetative parts were removed and the listed items in the end were put into the text in a much better context. Also, now that the name of the system involves "lineage" (and a lot of focus is put on it in the start) the terms data provenance and lineage were defined in the definition section. Some other intersting points that I encountered during the research on definitions were added to the discussion and final lists, and the DOI of one reference paper was corrected.
2020-03-23Analysis and configuration file sections completeMohammad Akhlaghi-43/+148
With this commit a description of these two important parts have been added to the project, along with several figures showing various parts of the files that are discussed. I also done some other restructuring of the figures and files to make things fit better into the the description of the paper.
2020-03-08Menke+20 example: properly count number of papers with softwareMohammad Akhlaghi-0/+1
Until now, I was mistakenly multiplying the fraction of papers in that journal. This is corrected with this commit.
2020-03-08Edited description of example subMakefile for analysis-1Mohammad Akhlaghi-22/+34
In order to make the description more clear and readable, the rules in the demonstrated Makefile (and their links to the data lineage plot) were made more clear.
2020-03-02Described the first analysis phase with a demo subMakefileMohammad Akhlaghi-60/+240
Until now, there was no explanation on an actual analysis phase, therefore with this commit an example scenario with a readable Makefile is included. The Data lineage graph was also simplified to both be more readable, and also to correspond to this new explanation and subMakefile. Some random edits/typos were also corrected and some references added for discussion.
2020-02-16Two values from the input dataset are now written into the paperMohammad Akhlaghi-1/+2
This was done just to get going with describing the analysis process.
2020-02-15Edits in text, added Menke+2020 as a referenceMohammad Akhlaghi-56/+92
The text was slightly improved/edited and I also recently came up to the Menke et al. 2020 (DOI:10.1101/2020.01.15.908111) which also has some good datasets we can use as a demonstration here.
2020-02-07Edited parts of the textMohammad Akhlaghi-109/+153
While reading over the already written parts (and hopefully complete the paper), they were edited/corrected to be more clear.
2020-02-06Minor edits to various partsMohammad Akhlaghi-56/+82
Some edits were made after rereading of some parts.
2020-01-27Analysis phase description started with Final paper and verificationMohammad Akhlaghi-11/+108
With this commit, the general outline of the analysis phase is given, as well as a description of the LaTeX macros and their relation to the paper and thier verification. Also, the data-lineage figure was updated to have references.tex also and some resizing of the folders in file-architecture to be more clear.
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