Bioinformatics

Related Stories:

Learning

Biology

Bioinformatics

Bioinformatics Mon Nov 20 2017 22:00:17 GMT+0000 (UTC)
WHERE THE PARTY'S AT -- A post by on the Plaza blog Expanded access to images in the Biodiversity Literature Repository has prompted me to write up a little toy I created earlier this week. The Biodiversity Literature Repository (BLR) is a repository of taxonomic papers hos
Spoiler alert of the answer: it depends. In this post, Ill trace it back to how we got to that conclusion and refine it to what it depends on. There are several conceptual modelling languages with extensions for temporal constraints that then will be
SpaceX just launched and landed another two rockets over the weekend. I dont get tired of watching those images of re-entry and landing. The precision is mesmerizing and extremely inspiring. Leading a research group in academia I often look at resear
The R language provides many different tools for creating maps and adding data to them. I’ve been using the leaflet package at work recently, so I thought I’d provide a short example here. Whilst searching for some data that might
Sometime in 2009, I began listening to a science podcast titled This Week in Virology, or TWiV for short. I thought it was pretty good and listened regularly up until sometime in 2016, when it seemed that most episodes were approaching two hours in d
Part-whole relations seem like a never-ending storyand it still doesnt bore me. In this case, the ingredients were the taxonomy of part-whole relations [1] and a couple of foundational ontologies and the aim was to link the former to the latter. But
Day three of TDWG 2017 highlighted some of the key obstacles facing biodiversity informatics. After a fun series of "wild ideas" (nobody will easily forget David Bloom's "Kill your Darwin Core darlings") we had a wonderful keynote by Javier de la Tor
Why do some mutations cause cancer in some tissues and not others ? What happens to the cell signalling pathways during differentiation ? Why are some genes essential in some cell types and not others or why are some drugs more effective at killing s
A reminder that when idle queries pop into your head, the answer can often be found using R + online data. And a brief excursion into accessing the Weather Underground. One interesting aspect of Australian life, even in coastal urban areas like Sydne
Temporal conceptual models, ontologies, and their logics are nothing new, but that sort of information and knowledge representation still doesnt gain a lot of traction (cf. say, formal methods for verification). This is in no small part because model
The following is a guest post by Bob Mesibov. Do you know the party game "Telephone", also known as "Chinese Whispers"? The first player whispers a message in the ear of the next player, who passes the message in the same way to a third player, and s
I know that 17 years is not a very round number. It is also fairly arbitrary as I am assuming systems biology started around 2000 (see below). I was last week in Portugal, where every year for the past 8 years I have been teaching a week long course
Infographics. I’ve seen good examples. I’ve seen more bad examples. In general, I prefer a good chart to an infographic. That said, there’s a “genre” of infographic that I do think is useful, which I&
Exactly a year ago I did a mini-experiment to see whether search engine bias exist in South Africa as well. It did. The notable case was that Google in English on Safari on the Mac (GES) showed results for politically interesting searches that had le
Lets rise up to unite taxonomy and technology - I thought it already was? @rdmpage https://t.co/AkNz1GYGbw— Sjrur Hammer (@sjurdur) August 26, 2017 Holly Bik (@hollybik) has an opinion piece in PLoS Biology entitled "Lets rise up to unite t
Cancer datasets as a resource to study cell biologyThe amazing resources that have been developed in the context of cancer biology can serve as tools to study "normal" cell biology. The genetic perturbations that happen in cancer can be viewed almost
I keep seeing years represented by coloured bars. First it was that demographic tsunami chart. Then there are examples like the one on the right, which came up in a web search today. I even saw one (whispers) at work today. I get what they are trying
If you have read any of the blog posts on (automated) natural language generation for isiZulu, then youll probably agree with me that isiZulu verbs are non-trivial. True, verbs in other languages are most likely not as easy as in English, or Afrikaan
I've been viewing Apple's Knowledge Navigator concept video from 1987 and it's striking how much of this we have today, and yet how far away we are from the complete vision. For some background on this promotional video see The Making of Knowledge Na
It has been 4 years since I started as a group leader at the EMBL-EBI (see past yearly reports 1, 2 and 3). This year the group composition has been mostly stable, with the exception of interns that have rotated through the group. We had Bruno Ariano
First there was “insert statisticalmethod here“. Now we have R – making it easy “to do analysis stuff“. Via Elisabeth; I’ll hand you over now for an entertaining summary. To be fair, analysi
Despite the best intentions, I did not get around to writing a post on the paper that I presented last week at the First International Conference on Language, Data and Knowledge 2017, 19-20 June, Galway, Ireland, and now Paul Groth also beat me to it
GBIF is running its Ebbe Nielsen Challenge for the third successive year. This year the title is Liberating species records from open data repositories for scientific discovery and reuse. To quote from the Challenge background on Devpost: This year's
ISMB (Intelligent Systems for Molecular Biology – which sounds rather old-fashioned now) is the largest conference for bioinformatics and computational biology. It is held annually and, when in Europe, jointly with the European Conference o
Besides the full paper on heterogeneous alignments for 14th Extended Semantic Web Conference (ESWC’17) that will take place next week in Portoroz, Slovenia, we also managed to squeeze out two demo papers. You may already know of TDDonto2 wi
Yes, this post is indeed an attempt to fit as many buzzwords that I don't really understand into the title. I've been playing around with Glitch, which is a delightful project from Fog Creek (makers of Trello and co-creators of Stack Overflow). On fi
July 21-22 saw the 18th incarnation of the Bioinformatics Open Source Conference, which generally precedes the ISMB meeting. I had the great pleasure of attending BOSC way back in 2003 and delivering a short presentation on Bioperl. I knew almost not
Representing information and knowledge often can be done in different ways even when the same representation language is used. In some cases, one way of representing it is always better than anotheror: the other option is sub-optimal or plain wrongbu
Last week I was at WikiCite 2017, a fascinating three day event in Vienna. Wikicite is "a proposal to build a bibliographic database in Wikidata to serve all Wikimedia projects", and is attracting increasing attention from academics, librarians, publ
Highcharts has long been a favourite visualisation library of mine, and I’ve written before about Highcharter, my preferred way to use Highcharts in R. Highcharter has a nice simple function, hcboxplot(), to generate boxplots. I recently ge
Its a topic that never failed to generate a discussion on all 10 instalments of the ontology engineering course I taught from BSc(hons) up to participants studying toward or already having a PhD: those pesky definitions of what an ontology is. To top
In preparation for WikiCite 2017 I'm looking more closely at extracting bibliographic information from Wikispecies. The WikiCite project "is a proposal to build a bibliographic database in Wikidata to serve all Wikimedia projects". One reason for doi
“‘Demographic tsunami’ will keep Sydney, Melbourne property prices high” screams the headline. While the census showed Australia overall is aging, there’s been a noticeable lift in the number of peopl
I cant resist adding another instalment of brief reviews of some of the books Ive read over the past year, following the previous five editions and the gender analysis of them (with POC/non-POC added on request at the end). This time, there are three
At present BioStor provides a simple display of an article extracted from BHL. You get the page images, and sometimes a map and an altmetric "donut". But we can do better than this. For example, I'm starting to experiment with displaying a list of li
Back in February, I wrote some R code to analyse tweets covering the 2017 Lorne Genome conference. It worked pretty well. So I reused the code for two recent bioinformatics meetings held in Sydney: the Sydney Bioinformatics Research Symposium and the
Following on from previous posts The Semantic Web made fun: d3sparql and The Biodiversity Heritage Library meets Wikidata via Wikispecies: adding author identifiers to BioStor I've put together an example query that can be used to extract a taxonomic
Just pushed an updated version of my nhmrcData R package to Github. A quick summary of the changes: In response to feedback, added the packages required for vignette building as dependencies (Imports) – commit Added 8 new datasets with fund
I've added an experimental feature to BioStor that uses data from Wikidata and Wikispecies to augment what information BioStor displays on authors. This is a crude first step towards the goal of representing all the data in BioStor as a "knowledge gr
Do you like R? Information about Australian biomedical research funding outcomes? Tidy data? If the answers to those questions are “yes”, then you may also like nhmrcData, a collection of datasets derived from funding statistics p
Short version: if RStudio on Windows 7 crashes when viewing vignettes in HTML format, it may be because those packages specify knitr::rmarkdown as the vignette engine, instead of knitr::knitrand you’re using rmarkdown v1. Longer version wit
Things to know about Lorne in the state of Victoria, Australia. It’s situated on the Great Ocean Road, a major visitor attraction and a great way to see the scenic coastline of the region It’s home to a number of life science conf
It would be remiss not to mention briefly the passing of Hans Rosling. Data needs storytellers and the world needs advocates for evidence-based decision making. We have lost one of the best. For some insights into the man and his interesting (and at
Dual y-axes: yes or no? What about if one of them is also reversed, i.e. values increase from the top of the chart to the bottom? Judging by this StackOverflow question, hydrologists are fond of both of these things. It asks whether ggplot2 can be us
Yes, it started with a tweet: Nice graphic on urine components via https://t.co/sfuXNB02sF pic.twitter.com/vhVLahQ8su — Metabolomics (@metabolomics) January 31, 2017 By what measure is this a “nice graphic”? First, the J
Like many data nerds, Im a big fan of Tyler Vigen’s Spurious Correlations, a humourous illustration of the old adage “correlation does not equal causation”. Technically, I suppose it should be called “spurious
So the votes are in: Your established blog is mostly about your work. Your work changes. Do you continue at the current blog or start a new one? — Neil Saunders (@neilfws) January 23, 2017 I thank you, kind readers. So here’s the
In this post: a brief summary of what I got up to, work-wise, in 2016 and my plans for a rather different 2017. The short version: it’s goodbye bioinformatics and hello educational data science! It feels as though 2016 was a challenging yea