11 replies to this topic

[Snowflake]

Hello everybody!

I programming some Biotools (Blasting, Ligation, Alignments, RNAi off-target, PCR etc.) in my free-time, mostly for Windows.

I have a question whether there is any interest for Linux users (esp. Ubuntu) to use such tools. The Ubuntu software center has a lack of scientific tools but before I start to port my programs, I would like to know whether there is an interest from the user site.

So how many of you have access/use Ubuntu for work?

Thanks for any comment!
Stefanie

[pito]

Not a lot of people use linux.
I guess as long as only a minority of people use linux, there will not be a lot of demand for such programs.

But arent some of those programs allready avaible for linux? BLAST for example is avaible for linux.

[Snowflake]

Yes, that's the point.
On the other hand people which develop Linux OS such as Ubuntu always complain about so less softwares in science which make Ubuntu uncomely for scientist.

Let see how many people reply here.

Thanks for your feedback!

[Dennis_Simpson]

I do use Linux but only for our databases and web hosting.  Analysis is almost entirely Windows.  I like Linux alot more than Windows but there just isn't much off the shelf science software available.

[hobglobin]

Population genetics people like to use Macs and some software was only available for this OS....so an alternative would be nice windows or linux, I don't care that much...just don't want to buy a Mac just to use a special software....

[toejam]

there are several options in linux such as https://www.scientificlinux.org/ or biolinux, which is based also on ubuntu http://nebc.nerc.ac.uk/

i prefer linux but i must admit that ms office looks better than libreoffice, at least now that i'm working on corrections for my thesis...

[bob1]

toejam, on 04 July 2012 - 10:00 AM, said:

i prefer linux but i must admit that ms office looks better than libreoffice, at least now that i'm working on corrections for my thesis...

LaTex FTW

[pito]

bob1, on 04 July 2012 - 05:42 PM, said:

toejam, on 04 July 2012 - 10:00 AM, said:

i prefer linux but i must admit that ms office looks better than libreoffice, at least now that i'm working on corrections for my thesis...

LaTex FTW

I was thinking the same thing.
However I must admit: I use word myself. Never took the time to lear latex and I wonder whether it really is that much better?
I have seen papers/PhD thesis etc in latex that didnt look better (at all) then those written in word.
It seems that Latex is only better if you need to use a lot of (chemical) formulas

[bob1]

pito, on 04 July 2012 - 11:11 PM, said:

bob1, on 04 July 2012 - 05:42 PM, said:

LaTex FTW

I was thinking the same thing.
However I must admit: I use word myself. Never took the time to lear latex and I wonder whether it really is that much better?
I have seen papers/PhD thesis etc in latex that didnt look better (at all) then those written in word.
It seems that Latex is only better if you need to use a lot of (chemical) formulas

I'm using latex for a lot of writing now, and I quite like it.  I find the way image and table placement works really nice, as well as the referencing (papers and table of contents sort of stuff) excellent.  i also like the way I can do a draft that just puts a box where the image will be and allows me to do the final sorting out of layout and content without slowing down the file by including the images each time.

[pito]

bob1, on 07 July 2012 - 10:53 AM, said:

pito, on 04 July 2012 - 11:11 PM, said:

bob1, on 04 July 2012 - 05:42 PM, said:

LaTex FTW

I was thinking the same thing.
However I must admit: I use word myself. Never took the time to lear latex and I wonder whether it really is that much better?
I have seen papers/PhD thesis etc in latex that didnt look better (at all) then those written in word.
It seems that Latex is only better if you need to use a lot of (chemical) formulas

I'm using latex for a lot of writing now, and I quite like it.  I find the way image and table placement works really nice, as well as the referencing (papers and table of contents sort of stuff) excellent.  i also like the way I can do a draft that just puts a box where the image will be and allows me to do the final sorting out of layout and content without slowing down the file by including the images each time.

I see what you mean.
But was it easy to learn? The reason I do not really use it, is because I just cant seem to find time or "courage" to start with it.. it seems difficult to start with and also: isnt it something you need to keep using in order to stay fast and good?

[bob1]

pito, on 07 July 2012 - 11:03 AM, said:

pito, on 04 July 2012 - 11:11 PM, said:

Latex stuff

I see what you mean.
But was it easy to learn? The reason I do not really use it, is because I just cant seem to find time or "courage" to start with it.. it seems difficult to start with and also: isnt it something you need to keep using in order to stay fast and good?

Yeah, it took a bit of time and effort to learn the basics, and I still have to go back and look up some things now and again, but the packages come with full documentation and there is an excellent wikibook online for geting most stuff right, not to mention googling just about anything will get you a useable answer (though not necessarily the best answer).  The hardest part i have found is getting a good package for doing the specialist things I want (e.g.writing chemical formulae, SI units, multiple page figures), as there are usually lots of options or different ways of doing things, which will give you more or less the same output but are more cumbersome/difficult to write.  For example you can write chem formulae by writing the letters and then entering math mode to make super/subscripts, or you can use a package such as mhchem and write \ce{formula here} and it will output it nicely.

I mostly got into it because i was sick of bloody endnote and word crashing when I was writing anything with over 100 refs or anything that was image heavy.

Drawbacks include having to get the context of your stuff just right for everything, remembering to put all the brackets in (though the processing will tell you when and where you have done this).  Having to have all the images in a separate folder forces you to have to come up with a useful naming system to avoid confusing yourself, which can be a bit of a pain and means you have to take all your images and copy them from the parent files (e.g. if you have a series of images of the same thing but only want one, you have to make a copy and put it intothe image folder).

[Snowflake]

For a first start I submitted an App for the Ubuntu App Showdown Contest:

http://snowflakestefanie.blogspot.de/

At the moment it is still under reviewing, I'll post the link as soon as it is in the Ubuntu Software Center. If you like try, comment and rate it