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o0i9u8z7
July 10th, 2012, 09:23 PM
Hello!

For the Ubuntu App showdown and to try out Quickly, I decided to port one of my scientific programs to Linux (most scientist are using Windows, at least in my environment). Now the contest is over and I'm really surprised how easy and comfortable Ubuntu and the Software Center make it for programmers to submit and share a software.

In general, I would like to bring all my tools I have written so far to Linux but the question is, who will use it? What do you think about it? Are there any biologist here, which are looking for more scientific tools (especially molecular biology such as Blast, Primer Design etc.)?

My first tool for the contest is described here:
http://snowflakestefanie.blogspot.de/

I would appreciated your opinion!

Kind regards
Stefanie

CrocoDuck
July 12th, 2012, 05:42 PM
Hi. I'm not a biologist, but a physics student. I think that any contribution on software is exquisite! There's always someone who need it, but more important: it makes both the open source and scientific comunity lively. In physics we are usually use linux and open source: algoritms operates on datas. If they doesn't work like expected, experiments can lead to bad conclusions. Software must be open source: everyone can control, adapt and fix it. Even if they aren't open source the programs are very useful for students: they make you able to view the things you are studing. So they are welcome! Of course, open source is better, as really scientifical (the comunity gives feedback on it)!

drmrgd
July 12th, 2012, 06:04 PM
Hello!

For the Ubuntu App showdown and to try out Quickly, I decided to port one of my scientific programs to Linux (most scientist are using Windows, at least in my environment). Now the contest is over and I'm really surprised how easy and comfortable Ubuntu and the Software Center make it for programmers to submit and share a software.

In general, I would like to bring all my tools I have written so far to Linux but the question is, who will use it? What do you think about it? Are there any biologist here, which are looking for more scientific tools (especially molecular biology such as Blast, Primer Design etc.)?

My first tool for the contest is described here:
http://snowflakestefanie.blogspot.de/

I would appreciated your opinion!

Kind regards
Stefanie

Although perhaps a bit more complex than simply piecing together GUI tools, what the Biology world really needs is better bioinformatics programs for things like Next Generation Sequencing. Right now the computation is not able to well keep up with the chemistry, and people are struggling to analyze and interpret the data generated from these NGS runs.

That, though, is a whole field of study, and may outside the scope of what you're asking :p

Nice work on the stuff you've done, though. I've bookmarked your blog site for future reference (I might be able to use some of these tools in future!).

o0i9u8z7
July 18th, 2012, 12:59 PM
Hi!

Thanks drmrgd and CrocoDuck!

I agree that we need more NGS tools but for a single hobby programmer it's not very realistic (needs validation etc.), so big companies or bioinformatic groups can do this better.

But I'll keep on going to bring my other tools to the software center, can not harm ;) And they are and will stay open source of course, as science should be!

Stefanie

Warthaug
July 18th, 2012, 06:01 PM
A good vector-deign/cloning tool would be nice, as the options are somewhat limited (although, IMO, the options out there on other OS's are not great). An easy-to-use statistical/graphing program would also be a boon (something like prism) - there are some really good statistics stuff on linux, but are not easy to learn/use tools. A well-designed and easy to implement data base for cell-lines, oligios, vectors, etc, would also be great. Again, linux has many tool applicable to these uses, but often requires someone with a great deal of computer literacy to implement (i.e. running a SQL server).

Bryan

o0i9u8z7
July 18th, 2012, 08:17 PM
Thanks Bryan, this are great ideas (some of them I have already coded...)!