17 July 2013

477. OpenChrom - Dempster

I don't want to get into writing software reviews, but given how much OpenChrom, an open source program for mass spectrometry which can open a range of proprietary formats, has evolved since I tried the release code-named Syringe (http://verahill.blogspot.com.au/2012/09/using-openchrom-to-open-aglient-d-esi.html) in September 2012, I think a brief update may be in order.

Essentially, OpenChrom now seems a lot easier and more natural to use.

The installation is the same as before (I've copied the old post below):

1. Install Java v1.7 (need > 1.6)
You can either use openjdk 7 or (Oracle) Java. See here for a general guide to installing Oracle/Sun Java.

As for openjdk, you can easily install it:
sudo apt-get install openjdk-7-jdk

(the openjdk-7-jre package is enough if you don't want the full developer's kit)

Anyway.

Make sure that you've selected the right version:
 sudo update-alternatives --config java
There are 7 choices for the alternative java (providing /usr/bin/java).

  Selection    Path                                            Priority   Status
------------------------------------------------------------
  0            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      auto mode
  1            /usr/bin/gij-4.4                                 1044      manual mode
  2            /usr/bin/gij-4.6                                 1046      manual mode
  3            /usr/bin/gij-4.7                                 1047      manual mode
  4            /usr/lib/jvm/j2re1.6-oracle/bin/java             314       manual mode
  5            /usr/lib/jvm/j2sdk1.6-oracle/jre/bin/java        315       manual mode
  6            /usr/lib/jvm/java-6-openjdk-amd64/jre/bin/java   1061      manual mode
 *7            /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java   1051      manual mode




2. Get openchrom
cd ~/tmp
wget http://aarnet.dl.sourceforge.net/project/openchrom/REL-0.8.0-PREV/openchrom_linux.gtk.x86_64_0.8.0-PREV.zip
unzip openchrom_linux.gtk.x86_64_0.6.0.zip
cd linux.gtk.x86_64/OpenChrom/
sudo mkdir /opt/openchrom
sudo chown $USER /opt/openchrom 
cp * -R /opt/openchrom
chmod +x /opt/openchrom/openchrom

Stick

alias openchrom='/opt/openchrom/openchrom'

in your ~/.bashrc and source it.




A few notes:
You can now start OpenChrom by running
openchrom
from the command line.

You can install plug-ins, e.g. to open Agilent files, by going to Plugins/OpenChrom Marketplace. Plugins will typically run for 30 days, but can be unlocked for perpetuity by adding a serial key, which is free. Add license keys by first registering on the openchrom website, going to http://www.openchrom.net/main/content/plugins.php, and clicking on the plugin you want a serial key for. You can then enter that key by going e.g. Window/Preferences/Converter in the OpenChrom software.

Everyone has their own idea of what a good piece of mass spec software should look like, and I suspect that OpenChrom caters to them all. Layouts are called Perspectives here. On the flip side, if you accidentally use a perspective that doesn't suit you, you may be incredibly frustrated until you figure out what's going on.

I like wsearch32, so my preferred view is to go to Window/Perspective Switcher -> Chromatogram MS (exact).

Opening spectra is much easier than before: now simply go to File/Open Chromatogram (MSD) and click on the file (or directory structure in the case of e.g. Agilent .D directories) and open:

Anyway, openchrom is getting better, is easier to use, and is still the only open source program that I know which can handle such an array of proprietary formats. Also, it can export data in both .csv and .xls formats, but you will need to install plugins for that, which is luckily very simple.


15 July 2013

476: Rehash: using a browser proxy via tunnel, through a router and with reverse ssh

I may have covered this at some point, but if so, I can't find the post.

Here's the situation:
You have a linux computer at work, which is behind a corporate firewall.
You have a router at home which runs an ssh server (e.g. running tomato).
You have a computer at home, which sits behind the router above.
You want to browse from home using the corporate network

In my case it's a little bit different -- I want to make a change to the router my office network (I have my own office) sits behind, and the easiest way to do that is by logging onto that router via http (it's a stock netgear router).

How to:
First, at work, connect to your home router using reverse ssh, so that all traffic on port 19999 on the router gets sent to port 22 on your work computer:
ssh -R 19999:localhost:22 root@myhomerouter

Later, at home, forward all traffic to port 8989 on your home computer to localhost:19999 on your router (which then gets sent to port 22 on your work computer):
ssh -L 8989:localhost:19999 root@192.168.2.1

We've assumed that the router sits on 192.168.2.1 from inside the LAN. Localhost here refers to your home computer, while localhost in the command before that refers to the router.

Then, in a different terminal, open a proxy through port 8989:
 ssh -D 8888 me@localhost -p 8989

Finally, you can now edit your browser/network settings to use a SOCKS proxy on port 8888 like you would with any other proxy.

475. How to get into a Chemistry PhD program in Australia -- or at least a reply from a prospective supervisor

Here's yet another non-linux post. I'm currently getting ready for the start of the new semester and teaching, and so haven't had much time to work on improving my computer skills.

Anyway.

I've been advertising for an international PhD student for the past 9 months and have so far only had one great applicant and three acceptable applicants. That's out of ca 200 applicants in total.

So what does 'acceptable' mean? In this case my use actually agrees with the literal meaning -- students which will stand a chance of being accepted to the PhD program. It also means students which I could imagine working with.

The formal requirements will likely differ between different institutions, and between supervisors. In addition, some supervisors may be looking for different personalities in their prospective hires, than others.

I don't think that I'm being unnecessarily harsh in evaluating applicants, as I've had colleagues review my shortlists and who have thought I've even been a bit too optimistic in my evaluations.

At any rate, if you are looking for a PhD, be aware that there are a lot of applicants out there, and only a limited amount of money and places, so you will want to spend some time on your application.

So here are a few of my thoughts:
Before reading, keep in mind that I understand that applying for a PhD, especially if you are from the developing world and applying for a PhD position in the industrialised world, can be very tough, and sometimes depressing. You don't receive a reply to most of your applications, and when you do, they responses are normally negative.


* Try to familiarise yourself with the formal requirements, and address them in the first paragraph in your email to a prospective supervisor. In the case of my uni, there are two main requirements:
-- an undergraduate degree equivalent to a first class honour degree in Australia
-- a sufficiently good score at the IELTS

That's it. However, the hubris of many universities in Australia mean that the first requirement is a significant hurdle. Typically, good grades are just the beginning. In addition to that, the applicant needs to hold a masters degree (by research) and have a couple of papers in ISI rated journals. Obviously almost none of our own undergraduate students would meet that, but there you go.

So in your first paragraph, state what unis you did your degrees at, what your cumulative GPAs (or equivalent) were, how many papers you have published and what you overall band score AND section scores on the IELTS (or TOELF) are.

At this stage, that's much more important than your background, your hobbies, or anything else. If you can't meet the minimum requirements for entry to the PhD program, everything else doesn't matter.

* Read the advertisement, and follow any instructions
I ask applicants to submit all their documents as PDFs. Yet, I get plenty of applications with .doc, .docx, jpeg etc attached. You didn't read the instructions -- will you be more careful as a PhD student? Remember that you competing against plenty of applicants that did read the instructions.

Did I ask for your IELTS results? Didn't attach or mention them in your email/CV? Not a good sign. Also, it means that you're probably not a candidate.

* Address the supervisor and the supervisor's research
I get way, way too many emails that start with  'Dear Sir', or 'Dear Professor' or even worse: 'Dear Sir/Madam'. Put my name in there. It'll show me that you spent at least a few minutes on personalising your email. If you don't make that effort, why should I make the effort of reading your email and looking at your documents?

Also, please do mention the research of the supervisor you are applying to. It doesn't need to be anything insightful or special, but just write something like: 'I find your research into catalytic activation of molecules in ionic liquids very interesting.' or 'I read your article in Green Chemistry, 2013, 10, 2345 and found it very interesting. In particular, I liked how it showed how the selectivity of blah blah blah'.

The reason is not that you are showing off your great scientific skills (you've got an undergraduate degree -- we don't expect much), but that it shows you spent a bit of effort writing your email and personalising it. Also, flatter -- in moderation -- can occasionally help (don't go overboard, so be careful -- too much makes you seem insincere).

* Don't cold-call
This should go without saying. I've had one student email me in the morning, then call me in the afternoon. That kind of behaviour is probably correct if you are applying for certain jobs in the Real World (marketing?), but not for a PhD in chemistry. It's a sure-fire way of annoying people.

* Don't send a linked-in invite
I don't have time to scroll through your profile and try to compile a CV for you. Send me your CV in pdf format instead. Also, I don't know you, and have no incentive to add you to my 'network'.

* Be careful about 'hobbies' and 'interests'.
To me as a potential supervisor they really don't matter (again, this is my personal opinion). I know that the idea is to show that you are a well-rounded individual, but knowing that you like 'travel' or that you consider 'internet browsing' a skill will not be the edge that gets you into a PhD programme.

* 'It can't help you, only harm you'.
Keep this in mind. Unless it's a piece of information required in the advertisement, or that you are absolutely certain will help your application, consider leaving it out. You may include it to highlight a particular skill or trait, but remember that a CV can be interpreted ambiguously, and your intent may not be obvious. Instead, what you feel shows how independent and committed you are, can be seen as being unfocussed, a difficult person to work with, or simply attract attention away from more important aspects of your CV.

* Attending lectures, conferences
In their CVs, some applicants include lectures by famous people that they've attended, or conferences that they've gone to.

Here's the problem for me: most first year PhD students struggle with the notion that doing the work is no longer enough. Doing the experiments, or following your supervisor's instructions, is not enough. To get a PhD you need to make that extra effort and making things work. And if it doesn't work, you put in 150% effort -- the extra 50% being extra-curricular work on finding a related project that will work. Life as a PhD student can be easy if you are lucky, but most often is not -- life is incredibly good when you project is working, but on the flip-side it can be hard, depressing and demoralising when it isn't. You supervisor can alleviate some of that, but remember that your supervisor is only there to point you in a general direction -- the PhD is all about making the transition to becoming an INDEPENDENT research.

So be careful -- if you've presented posters or given talks at conferences or at other universities, you should definitely list them, but under a suitable heading -- NOT publications. They'll detract attention from the publications, and the publications is what will get you an offer of acceptance.

* Do not make things conditional
I had an applicant who was borderline (in terms of meeting the requirements), and in those cases occasionally the supervisor putting in extra effort into cajoling the university administration MAY be enough to get a student accepted (don't count on it). If your prospective supervisor asks you to re-take IELTS, don't write something along the lines of  'I will, but only if this is the last hurdle'.

I understand it's expensive, but remember: even if you meet all the requirements I cannot guarantee that you get accepted. And I can' wait months for each student to pass through the application system -- I need to hire someone now. So be proactive.

* Face-to-face (or skype/video) interview is a good sign
If your supervisor asks for a skype interview, this is a great sign. And likely this isn't really done in order to gauge your scientific skills, but just to get a feel for your personality. Also, it's a way of making sure that your English levels are good enough that you can communicate with your supervisor. Finally, if you are borderline in terms of IELTS/TOELF, your supervisor may be able to argue that you English is good enough based on that interview. So take the opportunity.

And send an email a few hours after the interview thanking for the opportunity. 1-2 lines is enough. It will show that you're a decent human being.

* Be prompt in replying to emails
It doesn't matter what stage of the application you are at -- until the paperwork has been signed you are still on probation. If you take several days to reply to any of my emails, then you are likely to be dropped. The reason is simple: if you take a week to get things done when you are a PhD student, then you will be a disaster for me. A disaster that I'll have to live with for the next 3-4 years, and whom will be using up my research grant, and potentially ruining my career.

I understand that the reason for you being slow may be different -- maybe you are just nervous, maybe you have nothing to say, maybe you feel you are intruding. Still, be prompt.

So:
if you can show that you can read and follow instructions, and if you can make my life easy by addressing the selection criteria in a clear way, and if you seem like a person I might enjoy working with for the next 3-4 years, then you stand a fair chance of getting an offer.

If I think you'll need constant supervision, is sloppy and won't follow instructions, or that our personalities will clash, I'll probably avoid you no matter how good your grades are.