OPIG’s growing immunoinformatics team continues to develop and openly distribute a wide variety of databases and software packages for antibody/nanobody/T-cell receptor analysis. Below is a summary of all the latest updates (follows on from v1.0 and v2.0).
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A match made in heaven: academic writing with latex and git
Alternative titles:
- A match made in
heavenhell: academic writing with latex and git - Procrastinating writing by over-engineering my workflow
If you are like me, you can happily write code for hours and hours on end but as soon as you need to write a paper you end up staring at a blank page. Luckily, I have come up with a fool proof way to trick myself into thinking I am coding when in reality I am finalling getting around to writing up the work my supervisor has been wanting for the last month. Introducing Latex and git- this was my approach to draft a review paper recently and in this blopig post I will go through some of the ups and downs I had using these tools.
Continue readingSupercharge Your Literature Review With These Tools
When starting a new project, conducting a literature review of the field can be one of the most daunting prospects. Not only do you need to get through a mountain of research papers, you also need to work out which mountain of papers to get through. You don’t want to start a project only to realise a few weeks (or months!) in that you missed a key paper which would have completely changed the course of your research. Luckily, there are now several handy tools which can help speed up this process.
Continue readingTackling horizontal and vertical limitations
A blog post about reviewing papers and preparing papers for publication.
We start with the following premise: all papers have limitations. There is not a single paper without limitations. A method may not be generally applicable, a result may not be completely justified by the data or a theory may make restrictive assumptions. To cover all limitations would make a paper infinitely long, so we must stop somewhere.
A lot of limitations fall into the following scenario. The results or methods are presented but they could have extended them in some way. Suppose, we obtain results on a particular cell type using an immortalized cell-line. Are the results still true, if we performed the experiments on primary or patient-derived cells? If the signal from the original cells was sufficiently robust then we would hope so. However, we can not be one hundred percent sure. A similar example is a method that can be applied to a certain type of data. It may be possible to extend the method to be applied to other data types. However, this may require some new methodology. I call this flavor of limitations vertical limitations. They are vertical in the sense that they build upon an already developed result in the manuscript. For certain journals, they will require that you tackle vertical limitations by adapting the original idea or method to demonstrate broad appeal or that idea could permeate multiple fields. Most of the time, however, the premise of an approach is not to keep extending it. It works. Leave it alone. Do not ask for more. An idea done well does not need more.
Continue readingNew review on BCR/antibody repertoire analysis out in MAbs!
In our latest immunoinformatics review, OPIG has teamed up with experienced antibody consultant Dr. Anthony Rees to outline the evidence for BCR/antibody repertoire convergence on common epitopes post-pathogen exposure, and all the ways we can go about detecting it from repertoire gene sequencing data. We highlight the new advances in the repertoire functional analysis field, including the role for OPIG’s latest tools for structure-aware antibody analytics: Structural Annotation of AntiBody repertoires+ (SAAB+), Paratyping, Ab-Ligity, Repertoire Structural Profiling & Structural Profiling of Antibodies to Cluster by Epitope (‘SPACE’).
Continue readingWriting Papers in OPIG
I’m dedicating this blog post to something I spend a great deal of my time doing – reading the manuscripts that members of OPIG produce.
As every member of OPIG knows we often go through a very large number of drafts as I inexpertly attempt to pull the paper into a shape that I think is acceptable.
When I was a student I was not known for my ability to write, in fact I would say the opposite was probably true. Writing a paper is a skill that needs to be learnt and just like giving talks everyone needs to find their own style.
Before you write or type anything, remember that a good paper starts with researching how your work fits into existing literature. The next step is to craft a compelling story, whilst remembering to tailor your message to your intended audience.
There are many excellent websites/blogs/articles/books advising how to write a good paper so I am not going to attempt a full guide instead here are a few things to keep in mind.
- Have one story not more than one and not less – when you write the paper look at every word/image to see how it helps to deliver your main message.
- Once you know your key message it is often easiest to not write the paper in the order the sections appear! Creating the figures from the results first helps to structure the whole paper, then you can move on to methods, then write the results and discussion, then the conclusion, followed by the introduction, finishing up with the abstract and title.
- Always place your work in the context of what has already been done, what makes your work significant or original.
- Keep a consistent order – the order in which ideas come in the abstract should also be the same in the introduction, the methods, the results, the discussion etc.
- A paper should have a logical flow. In each paragraph, the first sentence defines context, the body is the new information, the last sentence is the take-home message/conclusion. The whole paper builds in the same way from the introduction setting the context, through the results which give the content, to the discussion’s conclusion.
- Papers don’t need cliff hangers – main results/conclusions should be clear in the abstract.
- State your case with confidence.
- Papers don’t need to be written in a dry/technical style…
- …..but remove the hyperbole. Any claims should be backed up by the evidence in the paper.
- Get other people to read your work – their comments will help you (and unless it’s me you can always ignore their suggestions!)
Peer Review: reviewing as an early career researcher
Peer review is an important component of academic research and publishing, but it can feel like an opaque process, especially for those not directly involved. I am very fortunate to have been able to participate in the peer review of multiple papers, despite being very early in my career, through support from my supervisors and a mentoring program run by Sense about Science with Nature Communications. Here are some of the things I have learned.
Continue readingFragment-to-Lead Successes in 2019
In this blogpost, I want to highlight the excellent work by Jahnke and collaborators. For the past 5 years, they have published an annual perspective covering fragment-to-lead success stories from the previous year. Very helpfully, their work includes a table detailing the hit fragment(s) and lead molecule, together with key experimental results and parameters.
Continue readingGraphical abstracts that spark joy on a gloomy day
Have you ever read a paper just because it had a funny, endearing, or utterly bizarre graphical abstract? Ever since a colleague showed me the ‘Graphical abstracts that I gone and found’ Facebook page, I have definitely come across a few, and I thought I would share some of my favourite ones below. If you enjoy this kind of thing, I strongly suggest visiting their page for more – it makes for a wonderful distraction from pretty much anything. Continue reading
What can you do with the OPIG Antibody Suite? v2.0
Since my last blogpost on this topic back in 2018, OPIG has expanded its range of tools for antibody/BCR analysis. Here is an updated summary of the OPIG antibody databases and immunoinformatics tools.
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