Category Archives: Publications

Making your figures more accessible

You might have created the most esthetic figures for your last presentation with a beautiful colour scheme, but have you considered how these might look to someone with colourblindness? Around 5% of the gerneral population suffer from some kind of color vision deficiency, so making your figures more accessible is actually quite important! There are a range of online tools that can help you create figures that look great to everyone.

Continue reading

Converting pandas DataFrames into Publication-Ready Tables

Analysing, comparing and communicating the predictive performance of machine learning models is a crucial component of any empirical research effort. Pandas, a staple in the Python data analysis stack, not only helps with the data wrangling itself, but also provides efficient solutions for data presentation. Two of its lesser-known yet incredibly useful features are df.to_markdown() and df.to_latex(), which allow for a seamless transition from DataFrames to publication-ready tables. Here’s how you can use them!

Continue reading

A simple criterion can conceal a multitude of chemical and structural sins

We’ve been investigating deep learning-based protein-ligand docking methods which often claim to be able to generate ligand binding modes within 2Å RMSD of the experimental one. We found, however, this simple criterion can conceal a multitude of chemical and structural sins…

DeepDock attempted to generate the ligand binding mode from PDB ID 1t9b
(light blue carbons, left), but gave pretzeled rings instead (white carbons, right).

Continue reading

What can you do with the OPIG Immunoinformatics Suite? v3.0

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).

Continue reading

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 reading

Supercharge 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 reading

Tackling 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 reading

New 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 reading

Writing 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.

  1. 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.
  2. 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.
  3. Always place your work in the context of what has already been done, what makes your work significant or original.
  4. 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.
  5. 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. 
  6. Papers don’t need cliff hangers – main results/conclusions should be clear in the abstract.
  7. State your case with confidence.
  8. Papers don’t need to be written in a dry/technical style…
  9. …..but remove the hyperbole. Any claims should be backed up by the evidence in the paper.
  10. Get other people to read your work – their comments will help you (and unless it’s me you can always ignore their suggestions!)