Particle physics software

When starting out in high energy physics or, when getting a new computer, there’s some essential software and other useful apps to install. This list is provides short summary of software, mostly targeted at mac users.

Essential software:

  • ROOT is the standard data analysis framework used at CERN
  • XCode developer tools, usually pre-installed with OSX
  • TeXworks for word processing and other LaTeX applications
  • Vidyo for conference calls
  • XQuartz for X11 forwarding which may now come pre-installed on OSX

Useful software:

Research Hacks

To complement my recent blog posts Apps to boost your productivity and Increase your Research Impact, I have rediscovered a series of videos which summarise different ways that technology can be used to enhance your research! In addition to Research Hacks, the Learn Hacks series provides a few further resources aimed at student.

See the Research Hacks blog with a link to the videos here: Research Hacks – Short videos to help academics work smarter and maximise their impact and reach.

Pint of Science Sheffield

Sheffield hosted its first Pint of Science this year, where I was involved in the Atoms to Galaxies event “Making Contact”. Here’s a quick recap of the night!

Sheffield hosted its first Pint of Science at four venues around the city from May 23-25th 2016. I’d heard about previous Pint of Science events internationally, but had never attended any of the interesting science talks in the pub, so I was glad to volunteer in Sheffield.

The talks in each location were based on a theme with 8 out of the 12 events selling out! The themes and locations in Sheffield were:

  • Atoms to Galaxies at Bloo88,
  • Tech Me Out at The Roco,
  • Beautiful Minds at Harrisons 1884,
  • Planet Earth at The Doctor’s Orders.

Screen Shot 2016-06-09 at 21.30.38

I volunteered for the Atoms to Galaxies event “Making Contact” on the second night with talks from Simon Goodwin and Tareq Omairi. I’ve been involved in a number of science outreach events in the past so was really looking forward to the relaxed atmosphere and different setting for Pint of Science!

Atoms to Galaxies events in Sheffield for Pint of Science

Here’s a quick recap of the night!

Working alongside a team of volunteers and the event manager for the night, we arrived early at Bloo88 to get set up to make sure the night ran smoothly. It was the first time meeting the rest of the team but we had plenty of time to introduce ourselves and get familiar with our roles before people started to arrive.

The event kicked off at around 7.30pm with University of Sheffield Astrophysicist Professor Simon Goodwin, talking about extra-terrestrial life and techniques that are used to detect planets and life.

The second talk was by PhD student Tareq Omairi on his research sending balloons 40 km above the earth to collect samples to study microbes within our stratosphere. The photos below shows both speakers captivating the audience with their exciting research.

After each talk the audience had the opportunity to put their questions to the speaker, or to discuss further over a pint!

In addition to the talks, there were several activities. The Institute of Physics (IOP) provided a light painting tent to create images as shown below (one of my favourites made by one of the guests on the night).

My role was to help run the other activities which included a ‘Make an alien’ competition, using pipe cleaners! There were some really creative alien figures from the audience and other volunteers! Prizes were provided by the sponsors Mendeley and awarded for the best aliens and best light paintings!

In-house artist Samantha Galbraith captured the night with some wonderful illustrations! See twitter for even more from the night!

At the end of the night, the audience gave some great feedback on their evening in post-it form!

Overall the night was a success! It was great to learn about research in Sheffield outside of my field and it was very positive to have a sell-out event with enthusiastic attendees on the first Pint of Science in Sheffield. The event also couldn’t have happened without all of the hard work of the organisers, event managers and participants, thank you for all the great experience!

Unfortunately I didn’t get a chance to attend any other events but from the positive response and photos on twitter, Pint of Science, both in Sheffield and beyond, was full of interesting talks, discussion and activities! A great opportunity to showcase fantastic scientific research and spark some interesting questions.

Whilst I won’t be in Sheffield next year, I hope to be able to volunteer my help to Pint of Science in the future, either as an event manager or even potentially as a speaker! Science and a pint, what’s not to love!

Here’s how twitter responded globally to Pint of Science over the 3 days!

Pint of Science was attended by 160000 knowledge-loving people this year and I encourage you to get involved next year!


Academic writing resources

Academic writing can be a daunting task whether it’s papers, applications, conference notes or a chapter of your thesis. Whilst writing my thesis I attended as many seminars, talks and workshops as I could catered towards PhD students and researchers. Here’s a few tips and resources from these sessions which may be of use!

Getting started!

Plan your writing

Make a skeleton
Looking at a blank screen? Don’t know where to start? Make a list of your chapters or sections in your document. Adding headers with bullet points of what you plan to include can quickly amount to several pages, then, turning bullets into sentences and paragraphs is far easier.

Start with what you know
A lot of chapters may need checking values, acquiring or making images, reading papers, etc. I regret starting with the more challenging chapters as writing about what you know, your method, results gives you an extra burst of motivation and confidence. Maybe writing one paragraph of your research before reading complicated theory is the way to go.

Eat that frog!
When planning your day, the ‘Eat that frog’ concept by Brian Tracy aims to get the task you are most likely to procrastinate on, or the ‘worst’ task of the day out the way first thing in the morning, before you even have time to think about it. Then you can move through your day with ease! Read more about it here.

Project management
In my post Apps to boost your productivity, I list task management apps. If you have many sections or chapters to write, these apps may help you to plan your time effectively.
A potential use for these is to break down major tasks such as “Write Chapter 1” into many chunks which you can mark off to monitor your progress, such as list the papers to read, images to gather, sections to start, etc. Each time a task is complete, mark it off and move to the next one!

Schedule time to write

Write little and often
Aiming to write for a full day, or a full draft can be intimidating. Fitting small bursts of writing in, whether a few sentences, a paragraph or more can help you make progress.

Academic writing retreats
I discovered writing retreats half way through writing my thesis during Academic writing month (AcWriMo) and found them invaluable! Spending a morning, afternoon or full day writing in a quiet room with other people who are also writing helped me to really focus and get several thousand words down!
University of Sheffield organise monthly writing retreats (this webpage also contains lots of good resources!) but if you want to write more often then why not set up your own group with colleagues who also need time away to write!
The retreat is dedicated to writing: writing your intentions for the session, short discussion, write 1 hour, break 15 mins, writing 1 hour, write how you did, short discussion, or something similar! You can then see how many words it’s possible to write within this time and hopefully this will motivate you to write in short bursts often!

Pomodoro technique
The Pomodoro technique can be used to stay focused on your task of writing, breaking into 25 minute bursts and recording your progress. There are many apps and websites to help you with this, get searching!

Shut up and write Tuesdays, @SUWTues 
Similar to writing retreats, Shut up and write Tuesdays is a virtual community of academic writers who write on Tuesdays! I only discovered this recently so haven’t had a chance to try it out yet. But whether you want to join them, or read some tips and advice, take a look at their twitter.

The Writing Process


Read relevant papers
The best way to improve your writing style is to write more! But reading papers can be beneficial to improve your scientific language, familiarise yourself with the structure of papers and scientific writing style.

Manchester phrasebank
If you are stuck for words, Manchester phrasebank offers many phrases to help you get started, whether it’s an introduction, discussion of results or describing key concepts, there are plenty of resources on this website to help you make progress.

Choose a suitable word processor
There are many different options when it comes to word processors for academic writing.
Personally, I have used LaTeX for many years now, as is typical in my field. For papers, a skeleton document is often provided with style files for the specific journal.
Writing a major document I would recommend using some kind of version management software so that you can, at any time, revert back to a previous version or see what changes you have made, particularly useful for monitoring your progress!
I used svn to commit my TeX files and keep track of different versions, whilst github is another option with the same features.
Managing versions is also possible with Word, and GoogleDocs. Alternatively, Dropbox offers extended version history at an additional cost. Just gain a little experience on how it works before relying on it!


Reference Manager Software
As mentioned in Increase your Research Impact, on top of being a social network, Mendeley is a reference management tool which allows you upload and categorise papers which you may need to reference at a later date. I am yet to try using Mendeley for this purpose but there are many articles online with tips on how to use Mendeley as a citation tool, or other options for reference manager software!

Writing my thesis, I exported references as BibTeX items from online databases (eg. arxiv, Inspire, CDS) . Google scholar also offers this feature. I added all references to a single bib file with a useful, searchable name. I have used BibDesk in the past as a reference manager for Mac OSX, which allows you to upload papers to each entry and add additional details.

Reading references
When writing, your list of references soon accumulates… One very useful tip about reading references is to add a post-it (or note in your reference manager software) to each paper you read with a one-sentence summary about the main points and key words which might help you identify the paper at a later time. I used different colour post-it notes corresponding to each chapter with just a few words identifying key points, results or sections of use to help me, particularly when double-checking a value!

“Day off”

Using your list of tasks, tired days can still be productive by choosing less intense tasks to do however, don’t forget the importance of down time, doing things you enjoy, catching up with friends and SLEEP!


Increase your Research Impact

“Is my research making an impact?” is a question we all face as research scientists. Whether answering is for your own motivation, grant applications or public engagement, it is important to understand the outcomes and outputs of our research.

As a funded PhD student, I have recently had my first encounter with reporting the impact of my research and listing my publications, conferences I have attended, outcomes of my PhD, outreach events and so on. My immediate response to this was “ARGH WHAT DO I WRITE?” but after talking to other researchers with impact report writing experience and reviewing my CV that I had recently written, it was actually quite straightforward.

To make this even simpler, there are many different online profiles which allow you to upload your publications, interact with other researchers and which generate metrics to give you immediate insight into the impact of your research. The Impactstory blog offers a November Impact Challenge to introduce researchers to the many platforms available to increase research impact, visibility, professional networks and provide the tools to better evaluate impact.

Going through the blog posts, I have tried to summarise some of the useful tips and have set up several online profiles to test. The main points of the challenge focus on:

  • Find/upload your publications and citations
    Tools: Google scholar, Mendeley,, Researchgate
  • Follow updates of research of colleagues and new publications in your field
    Tools: Google scholar, Mendeley,, Researchgate, LinkedIn
  • Promote your research
    Tools: social media, blogs, press
  • Track your impact
    Tools: Google Analytics, Google scholar, Mendeley,, Researchgate, …

Researchgate and are very similar platforms, with the ability to upload/search for your publications, follow other researchers in your field, and read publications. They both also provide metrics with how many times your publications have been read, cited, etc.

Before signing up, it may be useful to see who within your network has profiles on each site, as I found that my publications were more accessible (ie. more people in my group/field) using Researchgate.

Mendeley is a free reference manager and social network which again allows you to upload or search for publications and use as a citation tool. I was unable to find many papers within my research interests, by using the “Particle physics” search. This suggests that I would need to manually upload interesting papers and my publications however the database has many, many papers covering a wide range of fields which may be useful for your research topic.

Google scholar profile searches automatically for online publications, adding them to your profile and notifying you when you have new citations or new publications. It is quite a basic platform, but for a list of publications and number of citations, very effective.

The above tools are all new to me. One problem I found is that there are no links between the individual platforms and no way to export your publications as a list. It would be very useful to be able to extract publications claimed on Google scholar and import to Researchgate or Mendeley rather than having to upload each publication individually.
EDIT 11/06/16: It’s really simple… goto your profile, click export, select all, ta-da!  
I find that Google scholar contains a more complete list of my publications.
When searching for my publications within Researchgate, I was able to “claim my profile” and it then provided many suggestions of other papers I am listed as an author however I had to sift through these, as it was also suggesting many papers with authors of similar names, which is the case also with Google scholar.

In contrast to testing new tools, I have been using LinkedIn for quite some time. I must admit I do not use it to its full potential and probably need to update my profile but it has some great features and allows you to connect with your professional network, write posts, list your publications, experience, skills and search for jobs. The difference between LinkedIn and the previously mentioned platforms is that it is designed to expand your professional network and increase your  visibility. It can be useful to get updates of the research of colleagues, but as most of the information is added manually, it is likely that many contacts do not keep this up to date. I’m not sure whether LinkedIn can be synced with the above platforms to automatically update your list of publications/skills/experience as they are added elsewhere.

Other ways to increase your impact from the Impactstory challenge include:

  • Set up an academic website
  • Science blogging
  • Social media
  • Data repository, software sharing (github), slideshare
  • Peer reviews

Finally, ORCID is another useful tool which assigns you a unique researcher identifier to allow people to find your publications using this ID. It can be beneficial if you have a common name or if you change your name. Again, I don’t yet see a way to import or sync your publications from Researchgate or Google scholar with ORCID but there are several search options, most of which require an additional account. [Edit: see edit above to export from Google scholar!]

I have had a very brief test of some of the platforms listed here. I’m sure there are numerous features which I am yet to discover. I would prefer if publications/citations could sync across the different platforms but as a basic insight into your publications, outcomes and widening your professional network, these networks might be a good starting point. For a complete list and introduction to setting up profiles, see Day 1 of the Impact challenge.

Do you use any of the above platforms? What features do you find most useful?

Apps to boost your productivity

There are many productivity apps and websites available to help you better organise your time, your projects and your PhD. Whilst I prefer putting pen to paper, saving information digitally and syncing it across all devices, and with colleagues, can make things easier.

During my PhD, I am yet to find my perfect method to maximise productivity but here are a few options I have tried and tested, which are worth considering.

  1.  Evernote
    At the start of my second year of my PhD I started using Evernote, adapting the  Getting Things Done (GTD) technique. Evernote is flexible, and relatively easy to use productivity app based on notes. Each note can sync over many devices where you can add to-do lists, attachments (PDFs, powerpoint, images, etc), and each note can be tagged and saved to specific notebooks. The search functionality within Evernote also enables you to find words from hand-written (or typed) documents, which can be a bonus providing your hand-writing is legible!

    I used several notebooks within Evernote, one for each project, and assigned tags related to the urgency and time scale of the work, for example today, tomorrow, this week, soon, some day, waiting. I also added weekly and monthly to-do lists and goals to keep track of work and to review my progress and was also able to share notes with colleagues.

    Screen Shot 2016-06-05 at 19.27.28
    Screen shot of the Evernote app in the web browser with a list of My Notebooks and a note I am viewing in the background. 


    Whilst using Evernote I had a free 1 year trial of Premium, which also meant that I could upload photos from my phone/tablet as searchable documents which was pretty handy if I made notes during a meeting I could upload to Evernote and link to my weekly review.

    I used Evernote for almost a year, however I do also like to keep a notebook and lab book and found that I was spending a lot of time just trying to write notes to keep Evernote up to date with what I was working on, also the app for Mac was quite slow to load which was frustrating when trying to find something in a hurry.

    Evernote also offers many other features I haven’t mentioned here including browser add-ons, and compatibility with other accounts such as gmail. Check out their website for a full list of features.

  2.  Bullet Journal
    The bullet journal is a simple and flexible way to stay organised with pen and paper. As a stationery lover, looking at bullet journals on pinterest/tumblr/instagram fills my life with joy. Sadly, I lack the artistic skill to make my bullet journal as decorative as ones you may find online and prefer to take a basic approach.

    When writing my thesis I had a small (A6) squared notebook that I carried with me everywhere which I’d just usually list 3 realistic tasks to complete that day and any events I was attending. This kept me focused and meant that I didn’t have one looming task that I kept putting off as it would be very specific and achievable. The notebook was dedicated only to PhD/thesis work so at the end of the day I could tick off the list and feel satisfied I had made progress.

    There are many different ways to ‘Bullet Journal’ and this technique can also work alongside other productivity tools.

  3. Wunderlist
    Wunderlist is a to-do list app which syncs over all devices. I first used the app in 2012 and it was an easy to use checklist app which has since incorporated many useful features including sharing and assigning tasks, categorising lists in folders, tagging, and more.
  4. Google Calendar
    I have used Google Calendar to sync events across all my devices throughout my PhD. It can also be useful to share your calendar and events with colleagues and to schedule time for particular tasks on your to-do list. Whilst I usually only schedule important meetings and tasks, you can also use the calendar for reminders and goals, and with the description and options to add attachments to events, it could also be used alongside google docs for collaborative work.

All of the above apps are free to use and are designed to increase your productivity, mainly in terms of note taking, to-do lists and task management. Searching in the app store, there are thousands of apps under the productivity category and I have barely touched the surface in my list here.

Other apps similar to Evernote:

Online notebooks, great for collaborative writing:

Task management apps:

I am really keen to try a task management app as I’ve read some really positive reviews. To be able to sync tasks with my calendar really appeals to me but I think that you need to use it as a group to gain all of the benefits of these apps.

On top of apps, I have also tried 100% paper-based organisation. Using a diary, lab book and many, many post-its. I prefer making notes on paper when at meetings and sometimes pen to paper helps ideas flow. I change my organisation system frequently, testing new methods but have not yet found a perfect method that works for me all the time.

Finally, worth a mention is IFTTT which is a digital recipe builder to automate tasks. It can be used with many of the above apps to make your life easier. For instance, to send reminders to colleagues, sync files automatically or create your own custom recipe to suit your needs.

What are your most used productivity tips? What apps do you use to keep on top of work? I’d love to hear what works for you, or what you think of some of the apps here!

Academic blogs

Are you trying to write your thesis but don’t know where to start? Or are you just starting or are mid-way through your PhD and feeling a little lost? Here are a few blogs which I wish I’d found earlier in my PhD which I can recommend for those moments you need reassurance or motivation.

James Hayton is a former physicist and since his PhD has written a book and regular blog posts about research and writing as a PhD student. He offers tips and advice particularly about the writing process and is a valuable source if you’re just starting out and don’t know what to expect, or even if you are in the final stages of writing up!

The Thesis Whisperer  hosts blog contributions written by former and current PhD students. It includes a vast range of resources, tips and advice from people who have been through the process themselves. Also The Research Whisperer is dedicated to research in academia.

Gradhacker (now blogging from here) features blog posts from graduate students covering a wide range of topics and Times Higher Education includes news and blogs which are often interesting for researchers.

The University of Sheffield Think Ahead Blog is written by the Researcher Professional Development team and offers relevant tips and advice for researchers. (Check your University or institute for similar websites!)

The Thesis Whisper also includes a post with a list of PhD blogs to follow!

There are also a few blogs which offer particle physics specific tips, such as for LaTeX, ROOT, or other programming languages. The blogs I have come across include:

[Note: I will add to this list on finding more websites, or if you have found any suggestions please send them my way!]

Quantum diaries
 follows the lives of particle physicists in both their work and daily lives. And PHD comics provides some light entertainment and relief when waiting for code to compile!

Image from University of Brighton