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Astrophysics Research Centre

School of Mathematics and Physics

Student handbook for undergraduate research projects

Welcome to ARC ! This is an introductory handbook for new students starting research projects within the Astrophysics Research Centre. You might be a final year MSci student or a summer placement student, or a even a beginning MPhil/PGR student and want some quick links to get you started and going. As students ask the same questions of their supervisor (what is a Mac and how do I see my files !) this is a quick start guide to get you going and will have some more detailed links to software, manuals etc. It is a living document and will updated by supervisors, and students as we answer your questions.

The scientific literature

You are about to do a research project. You work will be based on the history of scientific work in your field and putting your effort into context is the first step in realising how the scientific process works. Your science training to date will mostly have been through text books and repeatable undergraduate lab or computer based experiments. Now you need to consider the scientific work that has been published as papers. This will primarily put your work in context, but you will also have to critically assess what is written in the papers. You must judge the scientific content, either the data or the theory, and judge if the conclusions are supported by the data and analysis presented.

Fortunately you now do not need to stray from your desk to do this. The whole of the scientific literature in astronomy and astrophysics (and much of physics) is available through two sites

  1. NASA Astrophysics Data System (we call it ADS and this page describes it http://www.adsabs.harvard.edu/ ). It is very easy to use
    • Here is the search page : https://ui.adsabs.harvard.edu/ A useful tip is to find first author papers, use ^ before the name. So use author:"^Zwicky, F"
    • ADS links through to the PDF or online versions of the published papers. You can view these within QUB network, as we subscribe to all major journals. You will not get the most recent papers outside QUB, since the journals are commercial and do not make all papers open access. But the scientific community is totally committed to open access (the journals still want to make money), so we post our papers to the arXiv
    • The https://arxiv.org/ is the biggest open access project for science that exists. And virtually every physical scientist endorses it and thinks it's a good idea. Scientists post various versions of their papers here. Some post immediately they submit (i.e. before peer review), some submit only their accepted version after peer review. Some do both. But it is entirely traceable and open. Astrophysics is here https://arxiv.org/archive/astro-ph . Everyday there is a release of new papers in a daily listing. If and when you come to do a PhD, you will be checking this every day. Hardly anyone reads journal content listings anymore, hardly anyone goes to the library for journals, since you would be always 6 months out of date. And if your paper is not posted on arXiv, it will likely not get the recognition it deserves.

Your Linux computer - if you are using a PC

Essential tutorials - the linux/Unix command line and beginners python

You should complete these two tutorials :

The linux shell and command line : Code Academy link for tutorial

Python for beginners (you will need python to plot, and manipulate data) : https://www.codecademy.com/learn/learn-python-3

Your iMac - if you are using an iMac

You will be allocated an iMac and given a user name and password, this will only work on the specific iMac you are allocated. You may/may not change the password RSIR to advise!

Safari is the web browser - and you may setup the mail tool

The MacOS system is a Unix or linux based system, with more graphical user interfaces and easier installation for many packages and application. You can open a terminal and use it as a Unix/linux based system

If you a complete beginner, try this Code Academy link for tutorial

Basic tools are already installed, such as python, perl, C and Fortran compilers

You can install various useful bits of software from the Managed Software Centre - search for munki, and the window will pop up a menu of various applications. Useful things like ds9 , aquamacs for editing, evernote for sharing notebooks.

Terminal and linux based operating systems

If you have useful tutorials on bash and tsch use and scripting, then add here

Astronomical Software and Utilities

Installing IRAF through conda and anaconda on Mac

  1. The fastest way to get and install conda is to download Miniconda, a mini version of Anaconda that includes just conda and its dependencies : https://conda.io/docs/install/quick.html
  2. Go to OS X Miniconda install , download the Miniconda3-latest-MacOSX-x86_64.sh file and follow the online instruction which us basically one command : bash Miniconda3-latest-MacOSX-x86_64.sh
  3. Remember you need to open up a new terminal for this to take effect
  4. Next, install the IRAF software stack : http://astroconda.readthedocs.io/en/latest/installation.html
  5. Go to Legacy Software Stack (with IRAF) and follow instructions
  6. This will install the X11 software, which is the windowing system for graphics for IRAF and other tools
  7. Now open an xgterm from the terminal xgterm &
  8. cd to change dir to home
  9. And setup IRAF mkiraf choosing the xgterm as the perferred option

Dave's Young's explanation and alternative to installing conda, miniconda, astroconda etc. Having these pre-installed on your machine can really take the headache out of then installing the PESSTO pipeline or Orbfit and the likes.

IRAF tutorials :

  • Supervisors … please add here !
Cool Python stuff
public/ug_handbook/start.txt · Last modified: 2019/09/23 10:13 by Stephen Smartt

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