Software tool article --- progress

AsimHDar commented

2018-10-27 14:30:13 +00:00

(Migrated from github.com)

Hi! After going through the guidelines (https://f1000research.com/for-authors/article-guidelines/software-tool-articles) and samples I pieced together the sections/subsections that I think work and those that do not. Also added some content on page 2 (with minor edits) --- @mih let me know if it's generally moving in the right direction and any issues you may see.

AsimHDar commented

2018-12-03 21:51:35 +00:00

(Migrated from github.com)

TODO:

1) Write up implementation of algorithm

For software tool papers, this section should address how the tool works and any relevant technical details required for implementation of the tool by other developers

Explanation of how the algorithm works. We decided to also go over how the approach differs from other algorithms. Secondly, we wanted to make a diagram of how it operates (like how how the NH paper showed the peaks, etc)

2) Use cases

Examples of input and output files should be provided with some explanatory context. Any novel or complex variable parameters should be explained in sufficient detail to enable users to understand and use the tool's functionality.

a) NH algo vs REMoDNaV on Anderson dataset:
Decided on simple tables showing this data. Ultimately it will have the outputs from our algorithm, the NH algorithm and the human coders (which are the golden standard)

b) REMoDNaV output when applied to studyforrest dataset (i.e 2 different noise conditions)
Decided to make all the plots from the thesis, and more (lots of main sequences). Once we do this we can take a look at what we want to keep.

3) Discussion and conclusions of results
Should be brief. Simply going over the take home messages.

The format is pretty malleable (I checked a lot of accepted papers in this category) so we can decide to add/remove sections one needed. Also: gotta polish figures on inkscape/corel once they are finalized.

TODO: **1) Write up implementation of algorithm** > For software tool papers, this section should address how the tool works and any relevant technical details required for implementation of the tool by other developers **Explanation** of how the algorithm works. We decided to also go over **how the approach differs from other algorithms**. Secondly, we wanted to make a **diagram of how it operates** (like how how the NH paper showed the peaks, etc) **2) Use cases** > Examples of input and output files should be provided with some explanatory context. Any novel or complex variable parameters should be explained in sufficient detail to enable users to understand and use the tool's functionality. **a) NH algo vs REMoDNaV on Anderson dataset:** Decided on simple tables showing this data. Ultimately it will have the outputs from our algorithm, the NH algorithm and the human coders (which are the golden standard) **b) REMoDNaV output when applied to studyforrest dataset (i.e 2 different noise conditions)** Decided to make all the plots from the thesis, and more (lots of main sequences). Once we do this we can take a look at what we want to keep. **3) Discussion and conclusions of results** Should be brief. Simply going over the take home messages. The format is pretty malleable (I checked a lot of accepted papers in this category) so we can decide to add/remove sections one needed. Also: gotta **polish figures** on inkscape/corel once they are finalized.

AsimHDar commented

2018-12-03 21:58:23 +00:00

(Migrated from github.com)

Unsure whether we decided on making confusion matrices or not.

mih commented

2018-12-12 10:12:33 +00:00

(Migrated from github.com)

I have now pushed a pseudo-code-like description of the general algorithm flow.

👍 1

mih commented

2019-04-23 07:06:21 +00:00

(Migrated from github.com)