As a professor emeritus of computational medicine and bioinformatics (Michigan), citations are very important for promotion, but so are patents. Methods papers get more citations than experimental or clinical studies. (only 20K citations here - most of my life was in industry, or my own start-ups, or as a section chief at the NIH). Thanks, although you folks do not post often enough - I feel like I am responding to a video uploaded years ago. Good luck on OM Genomics Labs - look out for the amount of time you will have to spend with lawyers. Cheers - Gerry Higgins, Ph.D., M.D.
00:00 Introduction 00:41 Examples of well-maintained software 08:23 Maintenance after leaving 13:45 Web apps vs CLI 26:02 Running code client-side 33:50 Expected support duration 41:03 Other technical lessons 48:15 Fixing the current system
A software engineer researcher here. I work at a commercial metabolomics research lab that's a also a research lab at a university. And I do exactly what you were talking about around 57:00. I build projects (mostly webapps and databases and SaaS like services and bio related algorithms) and teach and mentor more junior "bio software engineers" who are mainly undergrad and grad students at the bio department, while they work on and maintain the older projects and learn at the same time. Edit: typo
@skantasha5678 Hey, Would it be cool if I connected with you on LinkedIn and get further advice from you? I'm currently building my own software tool as a tech in the lab to fulfill the labs needs, and get it published in a journal to eventually use that a ticket to spearhead my direction in bioinformatics. I wanted input on what would be good software engineering practices since I'm learning this as I go. I haven't listened fully to this video yet.
I try to cite each tool that I use for which the creator(s) of the tool would benefit from (or care about) a citation. If it's Microsoft Word, for example, I obviously would not cite it. But anything for which there is a paper, I try to cite it. I have never been asked to reduce my number of citations. I nearly always publish in online-only journals, so it has not been an issue for me.
I think webapps should be made as separate modules so that many CLIs can produce generic and simple outputs that are compatible with the UI module. But bioinformticians aren't good engineers, especially early on, when they create their most influential tools... 😅 Also, you could still dockerize your old tools today!
As a professor emeritus of computational medicine and bioinformatics (Michigan), citations are very important for promotion, but so are patents. Methods papers get more citations than experimental or clinical studies. (only 20K citations here - most of my life was in industry, or my own start-ups, or as a section chief at the NIH). Thanks, although you folks do not post often enough - I feel like I am responding to a video uploaded years ago. Good luck on OM Genomics Labs - look out for the amount of time you will have to spend with lawyers. Cheers - Gerry Higgins, Ph.D., M.D.
00:00 Introduction
00:41 Examples of well-maintained software
08:23 Maintenance after leaving
13:45 Web apps vs CLI
26:02 Running code client-side
33:50 Expected support duration
41:03 Other technical lessons
48:15 Fixing the current system
A software engineer researcher here. I work at a commercial metabolomics research lab that's a also a research lab at a university. And I do exactly what you were talking about around 57:00. I build projects (mostly webapps and databases and SaaS like services and bio related algorithms) and teach and mentor more junior "bio software engineers" who are mainly undergrad and grad students at the bio department, while they work on and maintain the older projects and learn at the same time.
Edit: typo
@skantasha5678
Hey,
Would it be cool if I connected with you on LinkedIn and get further advice from you? I'm currently building my own software tool as a tech in the lab to fulfill the labs needs, and get it published in a journal to eventually use that a ticket to spearhead my direction in bioinformatics. I wanted input on what would be good software engineering practices since I'm learning this as I go.
I haven't listened fully to this video yet.
@@josecantu8195 yeah sure
I try to cite each tool that I use for which the creator(s) of the tool would benefit from (or care about) a citation. If it's Microsoft Word, for example, I obviously would not cite it. But anything for which there is a paper, I try to cite it. I have never been asked to reduce my number of citations. I nearly always publish in online-only journals, so it has not been an issue for me.
I think webapps should be made as separate modules so that many CLIs can produce generic and simple outputs that are compatible with the UI module. But bioinformticians aren't good engineers, especially early on, when they create their most influential tools... 😅
Also, you could still dockerize your old tools today!
47:17