This is a great comment! Thank you!

> What are these metrics? Download statistics? Number of forks? Number of stars? How do they help 'shine a spotlight'?

I decided against going deeper into the description of what the hub would ideally look like, and what kind of metrics it would collect, because that is a vast topic by itself. Download statistics and distributed version control stats definitely come into play here (number of active contributors, open issues, frequency of updates, responsiveness to opened issues, etc.), but the main statistic is probably software citations. I'd like to spend some dedicated time to try and figure out which numbers (if any) are indicative of the quality of software, but I'm sure you're well aware of how difficult that task is. Do you have any suggestions perhaps?

> I co-authored the structure visualization program VMD. It included several third-party components, for example, the STRIDE program to assign secondary structures, and the SURF program to compute molecular surfaces. How would the original authors know about those uses?

That's the idea behind transitive credit. As long as you can read and parse the dependency tree, you can give credit to dependency authors, such as STRIDE and SURF. This can go multiple levels deep, in theory.

> If the software is indeed one of the best in class, then the department head right now can review citation statistics. What does the hub add?

I'd like to believe this to be true, but why is every researcher involved in writing code unhappy with how software is treated in academia. In sickle's case, for example, some authors don't use a regular citation and instead only use a link to GitHub (e.g. http://europepmc.org/articles/PMC4410666, ctrl+f sickle). This happens more often than you would think and is something that regular citation statistics just don't cover, and the hub can tackle easily.

> How does the department head evaluate if the researcher's contribution is significant to the overall project?

In software written using version control systems, it's at least a bit easier than in research papers. Which author's contribution is significant for the overall paper? Those problems remain the same, but due to the transparent nature of software, are perhaps at least more tangible here.

> Perhaps as good would is something like PubPeer, to allow reviews of the software.

That's absolutely true! And this can be easily added to the hub. It could be as much an automated collection process as a hand curated crowdsourced process. There has to be a good balance in there somewhere.

> More often, research software that people write is incredibly generic. "Call four different programs, parse their outputs, combine the results into a spreadsheet, and make some graphs." This might take a couple of weeks, and doesn't result in any publishable paper or good opportunities for code reused.

Perhaps that is true. But what I saw from experience (and what you can see for yourself if you search for e.g. github.com on EuropePMC http://europepmc.org/search?query=github.com) is that the software that is cited in papers is rarely generic. We can argue back and forth on this, but my theory is that what people reference in papers is a specific software-based piece of the puzzle that is novel. Would be nice to get some data on this. Stay tuned :)

> The task then is, which metrics would help a user make the right decision?

Searching for FTOOL's citation on Google Scholar (Blackburn, J. K. 1995, in ASP Conf. Ser., Vol. 77, Astronomical Data Analysis Software and Systems IV .. etc), versus WINGSPAN's citation, gives the following results: 170 cites for FTOOLS, and 0 for WINGSPAN. This is a metric that the hub could surface and make those decisions easier.

Again, thank you for the insightful comment!