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<p>Hi Tony,</p>
<p><br>
</p>
<p>I almost only use the terminal and do things in/from there, usually following a written protocol or a how-to guide. In that case it's not hard to find things as the protocols usually tell you what to type in. It's when I'm trying to find a program etc using
the clicky-button approach that I get lost (since I rarely use Bio-Linux as an everyday computer).</p>
<p><br>
</p>
<p>Perhaps when the day comes and I start using a Linux computer more regularly that will stop being an issue.
<img class="EmojiInsert" id="OWAEmoji8924" alt="😊" style="vertical-align: bottom;" src="cid:853cd446-bcb0-46cc-8d84-05629333e3db"></p>
<p><br>
</p>
<p>(Oh and thanks for all the brilliant work on Bio-Linux by the way!)<br>
</p>
<p><br>
</p>
<p>Sara<br>
</p>
<br>
<br>
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<div id="x_divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Bio-Linux-list <bio-linux-list-bounces@bioinformatics.org> on behalf of Tony Travis <tony.travis@minke-informatics.co.uk><br>
<b>Sent:</b> 27 April 2017 13:59<br>
<b>To:</b> bio-linux-list@bioinformatics.org<br>
<b>Subject:</b> Re: [Bio-linux-list] Bio-Linux Unity Desktop</font>
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<div class="PlainText">On 27/04/17 14:31, Sara Rassner wrote:<br>
> Hi,<br>
><br>
><br>
> >An advantage of choosing<br>
> >Ubuntu-MATE is that we would only need one set of training materials for<br>
> >local and remote use of Bio-Linux and MATE requires considerably less<br>
> >resources from the computer hardware than Gnome 3, which makes MATE more<br>
> >suitable for running on older laptops or desktop computers.<br>
><br>
><br>
> I think this is a very important consideration, since many of us are<br>
> running Bio-Linux in VB on desktop PCs, so freeing up resources for the<br>
> actual analysis is a good thing.<br>
<br>
Hi, Sara.<br>
<br>
I agree, and I debug Bio-Linux using a 'vanilla' install of the .ova in VB.<br>
<br>
I also find that putting VB disk images on SSD makes a BIG difference to<br>
performance!<br>
<br>
> For users, like myself, who don't have that much experience with Linux<br>
> and who are using Bio-Linux for bioinformatics only, it doesn't matter<br>
> too much which desktop is used, as long as software and files can be<br>
> easily found from the desktop. Personally, I prefer having both a menu<br>
> tree and a search box, so that I can find everything even if I'm not<br>
> sure where it is located or what it's called.<br>
<br>
One problem that people I teach do find with Bio-Linux, or any Linux, is<br>
that only the GUI programs are shown in the Unity Dash or on the<br>
Gnome/MATE Menu and they don't know where the command-line programs are.<br>
I've spent a lot of time trying to win the hearts and minds of Windows<br>
users, but there is simply no alternative to running some programs from<br>
the command-line and that's why I think that documentation is one of the<br>
most important aspects of the Bio-Linux project. Half of the Bio-Linux<br>
tutorial is dedicated to building a solid understanding of Linux, before<br>
trying to do any bioinformatics.<br>
<br>
The answer is, the command-line programs are on the PATH :-)<br>
<br>
I think some problems that Windows users have with Linux can be resolved<br>
by drawing an analogy between the Windows 'command' prompt and the Linux<br>
shell. However, you're right that people need to be able to find things<br>
easily. That's why we put local HTML documentation about all the<br>
software, including command-line programs, into Bio-Linux. However, we<br>
did not keep that documentation up-to-date as well as we should (I fixed<br>
it on my installed Bio-Linux, but not on the .iso).<br>
<br>
Thanks for your comments,<br>
<br>
Tony.<br>
<br>
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