In my opinion the biggest reason is the lack of incentive to maintain old software, which does not produce as many cotations/publications as working on something new. Since this would be very difficult to address, I don't see the state of things changing in the near future.
Hello, I have seen your video about the MacBook Air for bioinformatics. I really need your opinion regarding something please. Is it better to get the new MacBook Air m2 or new 13 inch pro m2 if I’m going to start my masters in bioinformatics? They’re both the same price, but I like the new air better so thinking about getting it. My only concern with the air is it doesn’t have a fan so it might heat up? I don’t know if the program’s bioinformatics and use might cause the laptop to heat up, or is that not an issue. Thank you so much, looking forward to your reply
Hi. I've been there too. To be honest I don't run heavy computations on my m1 mac pro and I didn't use those fans - only thing I can remember was a MSA on a big dataset of fastq (100GB) . Most of machine learning stuff I do is on google colab and when I had to do something for the Uni I used a cluster - but I know that not every student has such possibility. In my experience mac is a pain when you use dockers and deal with ancient bio software. If I would pick up a new laptop only for bioinfo I would rather go with linux than mac os - it is also standard for the industry in Eastern Europe :D
One more reason - a huge mess of dependencies. You'll be surprised how determined bioinformaticisns are to use specific versions of third-party libraries. And each of them is a trap waiting to be sprung on update...
Another suggestion: should also look more into containerization of bioinformatics workflows/software with Docker to make them more reproducible
I agree. Reproducible and harmonize for NGS pipelines, expecially.
This. Tonnes of resources out there for doing this and integrating it into your nextflow pipeline
In my opinion the biggest reason is the lack of incentive to maintain old software, which does not produce as many cotations/publications as working on something new. Since this would be very difficult to address, I don't see the state of things changing in the near future.
There is a Konrad Hinsen who blogs extensively about reproducing scientific software. I think this is very relevant to the video here.
Hello, I have seen your video about the MacBook Air for bioinformatics. I really need your opinion regarding something please. Is it better to get the new MacBook Air m2 or new 13 inch pro m2 if I’m going to start my masters in bioinformatics? They’re both the same price, but I like the new air better so thinking about getting it. My only concern with the air is it doesn’t have a fan so it might heat up? I don’t know if the program’s bioinformatics and use might cause the laptop to heat up, or is that not an issue.
Thank you so much, looking forward to your reply
Hi. I've been there too. To be honest I don't run heavy computations on my m1 mac pro and I didn't use those fans - only thing I can remember was a MSA on a big dataset of fastq (100GB) . Most of machine learning stuff I do is on google colab and when I had to do something for the Uni I used a cluster - but I know that not every student has such possibility. In my experience mac is a pain when you use dockers and deal with ancient bio software. If I would pick up a new laptop only for bioinfo I would rather go with linux than mac os - it is also standard for the industry in Eastern Europe :D
I am currently studying btech bioengineering 1st year, I just want ask if I can I do masters in computer science after my btech in the us ?
One more reason - a huge mess of dependencies. You'll be surprised how determined bioinformaticisns are to use specific versions of third-party libraries. And each of them is a trap waiting to be sprung on update...