Reference and Citation Management

Literature is the basis for research in any field. The past literature holds the key to what has been not done and has been never tried. With the new technological revolutions of the past two decades, we have noticed that number of papers being published has gone up in almost every field. This research publication explosion has led to a enormous stress on the researchers to keep track of the cutting edge research. So, there are software available to help us out in this messy jungle of journal articles.

Presently, many commercial and free citation management tools have emerged in the market. These software packages have their advantages and disadvantages. And of course, there is a bit of learning curve for each one of them. So, lets get on with our job of putting them together on one page! This is not the most thorough analysis and just based on my personal preference. Please pick the one you are most comfortable with and go on.

EndNote:
Proprietary Software from Clarivate Analytics

I have used EndNote from the very beginning in my college days until now. It is very reliable but doesn't have necessarily the best features. They release a new version every year. If your university has a subscription, it is worth having it. EndNote works best if you have not formed your library yet and are going to start fresh. I have had many problems with pdfs which I had already downloaded and making a working citation library out of them. It is well-established in the market so if you are downloading the citations from Web of Science and other related websites, you will get a standard citation format. It is easy to change citation styles and integrating it with MS Office. The pdf reader is a bit old-school and difficult to access as it is on the second tab of a reference.

Mendeley:
Free standard package with premium features at a cost
This software is amazing in terms of the importing pdfs and finding the relevant metadata. This works best if you already have downloaded different articles and want to bookmark them with their citations. They also have very good integration with MS Office and there is a good pdf reader with highlighting capabilities.

JabRef :
Open Source
Best for citation management using bib files and made specifically for the Latex bibliography management.Although it is a bit outdated and interface is not user friendly, but it helps in getting work done. You can very easily generate a bib file with auto-generated bibkeys.

Docear: 

This reference manager manages references along with a mindmap. It helps you find the connections between a number of references and understand what has been done and find the things which have not been done. This is for the super-organized researchers who need to know and track their references to do some Sherlock Holmes kind of reasoning as to why a particular topic needs to be explored.
You will find more details here :
Comparison between some reference managers

Zotero : Best for website bookmarking, storing online references, pdfs etc. Works best for people with extensive browser based research. The reference manager resides in your browser as an extension.
Allows to create citations in Word and OpenOffice and also tag your research. Also allows for collaboration

Advice: Swim or Sink in Research

I lose motivation every now and then. I try to find it by looking at different motivational blogs. But nothing motivates more than a fellow scientist telling you how to brace yourself for the daily troubles. Then, I chanced upon this golden advice(pdf) from Prof Steven Weinberg, a renowned Theoretical Physicist from University of Texas. It is very important to keep ourselves motivated in the research we are doing. I found his advice very useful. He focuses on giving a beautiful analogy to help us surf the vast ocean of Science literature which is increasing by leaps and bounds every year. It is easy to get lost and overwhelmed. I am not ashamed to admit that it happened to me.
So, in his own words, four important lessons you need to remember:

1. Sink or Swim - I must start doing research, and pick up what I needed to know as I went along.. To my surprise, I found that this works. I managed to get a quick PhD — though when I got it I knew almost nothing about physics. But I did learn one big thing: that no one knows everything, and you don’t have to. 
2. While you are swimming and not sinking you should aim for rough water -.My advice is to go for the messes — that’s where the action is. 
3. Forgive yourself for wasting time As you will never be sure which are the right problems to work on, most of the time that you spend in the laboratory or at your desk will be wasted. If you want to be creative, then you will have to get used to spending most of your time not being creative, to being becalmed on the ocean of scientific knowledge. 
4. Finally, Learn something about the History of Science,or at a minimum the history of your own branch of science. The least important reason for this is that the history may actually be of some use to you in your own scientific work. The best antidote to the philosophy of science is a knowledge of the history of science. 

This was just one step(discovering the origin of earth and sun) in a sequence of steps from Galileo through Newton and Darwin to the present that,time after time,has weakened the hold of religious dogmatism. Reading any newspaper nowadays is enough to show you that this work is not yet complete. But it is civilizing work, of which scientists are able to feel proud.

Excerpts from article published in Nature.

Another interesting quote is from Ira Glass which touches on the Writer's block which one faces soon after you engage in a creative activity. This dull phase, he states, will go soon. You have to fight your way through.

Ira Glass, American public radio personality

Nobody tells this to people who are beginners, I wish someone told me. All of us who do creative work, we get into it because we have good taste. But there is this gap.

For the first couple years you make stuff, it’s just not that good. It’s trying to be good, it has potential, but it’s not. But your taste, the thing that got you into the game, is still killer. And your taste is why your work disappoints you. 

A lot of people never get past this phase, they quit. Most people I know who do interesting, creative work went through years of this. We know our work doesn’t have this special thing that we want it to have. We all go through this. And if you are just starting out or you are still in this phase, you gotta know its normal and the most important thing you can do is do a lot of work. Put yourself on a deadline so that every week you will finish one story. It is only by going through a volume of work that you will close that gap, and your work will be as good as your ambitions. And I took longer to figure out how to do this than anyone I’ve ever met. It’s gonna take awhile. It’s normal to take awhile. You’ve just gotta fight your way through.          -Ira Glass

Gavin from Zen Pencils has made a beautiful illustration of this quote here.

Finally got a PhD, moving on to PostDoc: 2016 Here I come

Hi all,

Finally got a PhD in December and going for a PostDoc under my supervisor. It was indeed so happy and relieving. We struggle so hard and feel the stress of an impending boom and once you finish your defense and submit your thesis back. There is a fresh breath of air and you feel a lot better in terms of achievement and understanding the purpose of life.

I am continuing my academic saga for a while; before anything else drags me away. I hopefully can get some interesting results next year. Last year was a hell lot of year with hardly any money and mainly subsisting on support both moral and financial from friends and families. This coming year is promising and I hope I can reverse my trends upset by my PhD's low points. We have to dust ourselves up and move forward with a grit and determination to achieve the new heights.

Personally, I think I have a lot to learn in Photonics still. You can try to keep up as much, still the crowd around you keeps moving forward at an unimaginable pace. And one has to ensure to move with the crowd and not get left out. Learning is not enough. But achieving something new is more important.

Therefore, I have to set some personal goals to become better me next year. I hope if I speak them out publicly I will be more accountable. Without ado, here we go :

1. Get healthy
1. Get Exercise/Games Regularly  
2. Reduce my weight by 5 kgs
3. Get 7 hrs of sleep on time
2. Plan your work and work the plan
1. Don't wait for deadlines to fall on your head
2. Focus on one thing and wait for it to finish. Other things can wait. But finish this very thing and move on.
3. Write more and send more papers to the press
3. Get more organized : work/home/life 
1. Aim for balance
2. Reduce the extras and declutter : Just the essentials
4. Learn People skills
1. Art of delegation :Distributing the workload
2. Appreciation and motivation
3. Art of collaboration: Complement your abilities and work in unison to produce value
4. Present your work better

This would be my wishlist for becoming a better person next year academically and professionally.
Even if I get better in half of these things, I would be more efficient and these habits will boost my confidence. Hope it inspires you as well to formulate your own list. I will try to implement this even before the new year starts and hope to keep a tab on my progress. Observation is the key to the execution of these behaviors before they become habits. Once they become habits, we can sit back and routine will help us to do better subconsciously.
Alrighty then !

As a scientist, fooling yourself = failing yourself !

It is not uncommon in research to fall prey to make experimental data to fit your hypothesis instead of building a hypothesis based on the facts. There are many pitfalls in a scientific investigation and one must be wary of how you interpret and analyse your results. For a nice guide to avoid these fallacies, Nature has put this infographic in their news article.

Adapted from Nature

I learnt this from the following link: 

 http://conceptpickings.com/2015/10/13/scientific-methods-and-statistical-interpretations-to-believe-or-not-to-believe-that-is-the-question/