Should I publish my software independently or publish it along with a case study in higher journal? I have built a software that handles protein clustering data in specific format. It is able to draw several plots on that basis along with many other analyses. It has more options than its existing competitor. Should I just try to get it published as a software/technical issue, or try some
case study data (research work on a logical data) produced by the software
+
the software,
   in a better journal?
In my discipline (political science), one would typically do both. Write an applied article that uses the software for an actual research project and submit that to a substantive journal. Then, separately, describe the software and write it up for a software journal (e.g., Journal of Statistical Software, R Journal, etc.).