Hi Charlie,
Welcome to SEQanswers - thanks for getting so involved. Just to add a few cents about Windows and BASIC and to explain a bit about the IT focus here. Most people tend to use Linux and Unix-derived languages like Perl because they are open source and free, which is a big advantage in academia and elsewhere. This means the whole ecosystem of bioinformatics tools has grown up within Linux, and it is quite difficult to do complex tasks from Windows, because the tools just aren't available.
It is true that many biologists are still using Windows only, and to be honest it's a pain to tell them they have to use Unix to do a lot of cutting edge bioinformatics. But because Windows is a closed platform and quite hard to develop for, Microsoft lost the bioinformatics community a long time ago.
It would actually be great to find a cross-platform approach so biologists didn't have to retrain to use Unix - some people develop tools in Java for this reason. However, I'm not sure QBASIC is a great solution - you mention yourself that QBASIC cannot handle large files; this is fatal in bioinformatics these days! I find Perl is still a reasonable option; we actually teach Perl to biologists in two days and hopefully give them enough to be writing useful programs - and of course you can use ActivePerl or Strawberry Perl on Windows.
On the IT focus - you're right, this community is fairly focussed on good tools and pipelines, because we're trying to figure out how to analyse next generation sequencing data of all kinds, and so we stay pretty close to the raw data. Each of us will have our own interests, but as biology is so varied, it's unlikely that many of us share exactly the same high-level biological concerns. Plus we're having so much trouble with the raw data that there is really still a lot to talk about at this level! But you can always try asking some questions on these topics and see what responses you get.
Welcome to SEQanswers - thanks for getting so involved. Just to add a few cents about Windows and BASIC and to explain a bit about the IT focus here. Most people tend to use Linux and Unix-derived languages like Perl because they are open source and free, which is a big advantage in academia and elsewhere. This means the whole ecosystem of bioinformatics tools has grown up within Linux, and it is quite difficult to do complex tasks from Windows, because the tools just aren't available.
It is true that many biologists are still using Windows only, and to be honest it's a pain to tell them they have to use Unix to do a lot of cutting edge bioinformatics. But because Windows is a closed platform and quite hard to develop for, Microsoft lost the bioinformatics community a long time ago.
It would actually be great to find a cross-platform approach so biologists didn't have to retrain to use Unix - some people develop tools in Java for this reason. However, I'm not sure QBASIC is a great solution - you mention yourself that QBASIC cannot handle large files; this is fatal in bioinformatics these days! I find Perl is still a reasonable option; we actually teach Perl to biologists in two days and hopefully give them enough to be writing useful programs - and of course you can use ActivePerl or Strawberry Perl on Windows.
On the IT focus - you're right, this community is fairly focussed on good tools and pipelines, because we're trying to figure out how to analyse next generation sequencing data of all kinds, and so we stay pretty close to the raw data. Each of us will have our own interests, but as biology is so varied, it's unlikely that many of us share exactly the same high-level biological concerns. Plus we're having so much trouble with the raw data that there is really still a lot to talk about at this level! But you can always try asking some questions on these topics and see what responses you get.
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