Monday, 16 February 2015

Open data: Walking the walk

I've long been a supporter of open access for both data and publishing, but I have to admit that although I have almost exclusively published in OA (or hybrid) journals, my data has been known to languish on hard drives and only appear if someone actually asks for it.

Given that so much of the research that I do relies very heavily on other people providing easy, and public, access to their data, it's fairly hypocrytical of me to be so lax at putting my own data out there for the rest of the community to use.  That's why my new job is so exciting.

Last Monday I started a new job, in a new lab. It's not strictly a postdoc position and it's not attached to a research project (although I will probably be helping out with some analysis on the side). Instead the new job is as part of team aiming to create a database containing all of the data that has come out of the myriad projects from this lab and to make that data available to other researchers.  Given the heterogeneity of the data and projects, it looks like it will be a difficult, but interesting task and I hope that our success (see that optimism already) will encourage other labs to undertake similar projects.

I'll be updating the blog with accounts of roadblocks and successes as we go along.

Tuesday, 7 October 2014

Peer Review is still worth it (mostly)

In the last month I've had two reviews back on papers that I'd submitted to journals.  And they've been very different experiences.

The response to the first paper really knocked my confidence.  Reviewer two was happy with it to be published basically as is (a few minor corrections etc.). The other reviewer loathed it, and didn't mind saying so. They hated everything about it, the premise, the methods, the conclusions.  It basically came down to the fact that they thought that pretty much everything I've every done was massively flawed.

And it really knocked my confidence. I'm pretty certain it was from someone who is very established (although I don't have a name, and I don't really want to know even though I could then exclude them from being a reviewer in the future) and from someone who works on similar problems but has a different favoured angle.

I have eventually come back around to the idea that it's just one reviewer, and if you're doing interesting work, there's probably always going to be someone who doesn't like it. On a different run I could have had a different set of reviewers and a very different outcome.  And that's one of the main problems with peer review. When you're only asking a couple of people what they think, you're almost certain to get a different response to what you'd get when you asked another two people.

Apart from with the review I got back yesterday, I didn't. And it rather restored my faith in pre-publication peer review. Both reviewers gave us very similar notes, they weren't delivered in a demeaning way, they weren't personal attacks and they will definitely help improve the manuscript. So sometimes, pre-publication peer review really works.

I've heard noises around the internet about the abolishment of pre-publication peer review (not that I think that'll ever happen), but I'm still of the opinion that in general it helps make a manuscript better. And that bad reviewer of mine had every write to express their hatred of my work, although they probably could have phrased it in a slightly less soul crushing way.

I also, though, think that the increase in post-publication peer review is a great thing.  Papers often slip the net with big mistakes because the reviewers weren't the right people to spot those mistakes (you can't be an expert at everything) and the scientific consensus on a paper can be very different to that of a couple of people.

Thursday, 2 October 2014

Is twitter an academic pandora's box?

In the first week of my masters course, prior to starting my Phd, I had a conversation with someone about how I wanted to be a lecturer.  It hadn't crossed my mind that I might not make it, and since the other participant in the conversation had a lot more experience than me (she'd worked as a research assistant for ~ 10 years), she basically decided I was an arrogant idiot.

(n.b. I was quickly forgiven for being an arrogant idiot and we became good friends)

I did not really take anything much away from this conversation.  I continued my career as I'd planned, and it wasn't until I was applying for jobs toward the end of my second postdoc that I started to find it hard.  But I was still plugging away, pretty certain I'd get there in the end.

Recently (I mean literally the last month), it's all started to get a bit much. And I'm going to lay this squarely at this feet of one culprit. Twitter.

Don't get me wrong, I love twitter, I love the way it allows us to communicate our passions and to connect with the world in a way that was just not possible 10 years ago.  But if I were not able to connect with the world in this way, I could continue in ignorance and maybe I'd get lucky and make it.  But I know the odds are against me now, Pandora's box is open and there's no way back.

Some recent things I've found out about through twitter that are getting me down (in no particular order):

  • Early Career (and not so early career) Researchers trying to encourage publishers to follow an open access pathway with clear reasoning, which was totally ignored and dismissed by the publishers here and here.
  • The fact that the President of the American Society for Biochemistry and Molecular Biology thinks most of us are riffraff.
  • Being able to directly see how unlikely it is that I'll ever get a job as a PI, and the fact that I'd have a 12% better chance if I were a guy.
  • Talking to people about how academia still has a diversity problem (Follow #diversityjc on twitter to talk more about this)  Conferences in particular have a problem where they only get white male speakers. And many of them don't seem to think this is worrying.
  • The fact that academic freedom seems to slowly be being worn away.
  • The culture of being mean to each other seems to be rewarded far more than does helpfulness and supportive behaviour

For the last 10 years, I have loved working in academia. I felt at home here. I loved the opportunity to research interesting topics and to follow where that research took me, but after it took me to America, 3000 miles away from my family, I started to wonder if I might need more than academia is prepared to give me.

I haven't totally given up yet, but I need to find a way of getting a healthier relationship with this career and I'm not sure I can ever go back to the happy naive state I once had.

Thursday, 7 August 2014

My response to some of the Open Access Myths

This morning there was an #ECRchat on twitter about Open Access publishing.  It's prompted me to write this post because there seem to be some pervasive myths about OA which stick around despite OA advocates best attempts to dispel them .So here's my attempt with 2 of them. It may come across as kinda angry, that would be because it makes me kinda angry.

1. Open Access publishing is less prestigious.

This is the comment I loathe more than anything in debates about Open Access, because although I don't know about other fields, in Genetics it's just not true. I've ranked journals by Impact Factor despite it being a useless metric (debate for another time).

Nature Genetics - 29.6 - 6 month embargo, then Green OA encouraged
Genome Research - 14.4 - 6 month embargo, unless author pays
Molecular Biology and Evolution - 14.3 - Pay for OA
Genome Biology - 10.5 - Open Access
PLOS Genetics - 8.1 - Open Access
Genome Biology and Evolution - 4.5 - Open Access
European Journal of Human Genetics - 4.2 - Pay for OA
Heredity - 3.8 - 6 month embargo, then Green OA encouraged
PLOS ONE - 3.5 - Open Access

So from this list (which I promise I didn't cherry pick to make a point) you can see that other than the Nature journals (Nat. Gen. & Heredity) you either get Open Access as standard, or you can pay to have open access (a whole 'nother can of worms).

I don't think anyone would think that publishing lots in Genome Biology or PLOS Genetics is going to be bad for your career, so at least in genetics, it's just ridiculous to say that OA is less prestigious.

2. Open Access lowers standards

When people talk about this they are conflating a number of different topics: Open Access, Journals which publish without regard to the subject and whether it's 'cool' or not and spam journals.

Lets get spam journals out of the way.

It's not really a problem. Have you seen those emails? Why would you ever publish there? Sure maybe some early Phd students might get duped, but they should have advisors who would protect them from that sort of mistake.  If still in doubt, check to see if the journal is listed here:

So now we'll tackle the difference between OA and journals that publish without regard to fashion, impact, etc.

Most of these journals are open access, e.g. PeerJ and PLOS ONE. But there are plenty of Open Access journals that are really difficult to get into e.g. Genome Research and PLOS Genetics.  Are you really suggesting that the Open Access policy of PLOS Genetics is lowering standards?

Regardless of the journals policy as regards topic, all of these journals have rigorous peer review processes, and it's mostly the same people reviewing for a range of different journals, so there isn't a difference in quality of reviewer.  Some journals (such as PeerJ) are now publishing the review process alongside the article, so you can even check how rigorous it is.

All journals are different and as far as I can see, the only thing that is consistently different across the board between OA journals, and those which aren't, is whether they make your institution's library buy a subscription in order for you to read the articles.  Seriously, that's the whole difference.

Monday, 12 May 2014

Post Phd Story

While perusing twitter the other day I came across a post by Jacquelyn Gill asking about people's post Phd stories.  There are a lot of "why I left academia" stories and you inevitably hear about the superstar stories, but there are a whole lot of us in the middle who never tell their post Phd stories.

So here's mine, take what you will from it.

I did my Phd at the Brighton & Sussex Medical School, and I liked what I was doing there, but I couldn't see myself staying on for a Postdoc (I don't think my supervisors could either...), the topic was fine, but I wasn't really excited by it towards the end of my Phd, and my main supervisor & I used to rub each other up the wrong way.

I had 3 years of funding, so as the three years drew to a close, I started to look for another job.  I was writing up at this point, but I was still quite a way from having the thesis finished.

I applied for a couple of jobs, one at Nottingham University, where I wasn't shortlisted and one at the National Genetics Research Laboratory in Manchester.  It was a 'Clinical Bioinformatician' job (I wasn't really sure what that was, when I got the the interview it turned out it was pretty much a made up job title...) creating tools and teaching bioinformatics for the NHS.

I was offered the job, I took the job, and I moved to Manchester.  For ~ 6 months I was working at NGRL during the day and doing my thesis at night.  Having had no experience with patient centred bioinformatics/genetics, I didn't know how I would take to it.  It turns out, it's not really my thing.  I'm definitely more a blue skies researcher type. However, it was a great job to have while I was writing up my thesis (BTW, it's totally possible, to write up with a new job.  It's not fun, but it's totally possible).

A few months after I'd passed my viva, I decided to start looking around to see if there were any postdoc positions which might be more my style.  I wasn't going to just apply for anything as I was fairly happy in the current job.  Almost immediately, a job came up at Nottingham University (different PI and campus to the last job), I went down for an informal chat before applying and it seemed like a great position.  The PI encouraged me to apply, I did, and I was offered the job.

Three years has gone by since then and I'm now in a second postdoc at Rutgers University in New Jersey.  I'm trying to find either my own money or a lectureship and it's hard.  But I left academia once and came back, so I know that this is the life that makes me happy.  Maybe I'll leave again if things don't work out.  But right now I'm sticking it out.

Thursday, 9 January 2014

The restorative powers of a good conference

It's all been seeming a bit much recently. The year long slog to find a second postdoc, and then finding a really great position that forces me to live halfway across the world from my wife.

The plan for this year (publish enough to seem competitive for fellowships) was starting to seem unrealistic & I could see myself staring down the "what-else-could-I-do" route.

And then I came away to my favourite conference, met up with some old friends, met lots of new interesting people. And they all seem to think I can do this (or if not they're nice enough to do a good job of hiding their doubt!).  I always come away from a conference rejuvenated and with new ideas for what ever project I'm working on, but this conference has reignited my desire for this career. I want to be working with these people, researching the kind of things that make them (and me) excited.

I still know how hard it's going to be, but I've got my drive back, so thanks popgroup47!

Thursday, 12 December 2013

Does playing the publishing game make us hypocrites?

As I'm sure any scientist or academic who spends any time on the internet will know,   Randy Schekman (recent nobel prize winner) wrote an article in the guardian about how we shouldn't be publishing in 'Glamour mags' like Nature, Science and Cell.  Of course his caveat is that we should all publish in his not quite glamour mag (because its open access) e-Life.

Obviously, there's been a lot of talk on twitter about this...

I've seen a lot of "Hurrah!" responses and a lot of re-post with out much comment. But there's also an undercurrent of people who aren't as happy as might be expected.  Mick Watson wrote a really good blog post explaining why some people are annoyed at Schekman and feel he's a hypocryte and that we shouldn't be praising him for something that will ultimately help him out (i.e. get us to publish in his new journal instead).

While I really respect this position, I have to disagree.  While maybe he doesn't deserve praise exactly, we need these people.  He's won a nobel prize, he's published lots in these closed-access journal, his credentials are sorted. So now he has both power and nothing to lose, he can say what he likes.  

I know from trying to persuade my former Boss to go with PeerJ, that people in this position (not that he's won a nobel prize!) aren't always interested in change, they know the system, they've worked out how to do well in the system and while they don't have much to lose, they also don't have much to gain by changing it.  Those of us without much power (Phd student, postdocs, ECRs), we may be idealistic and really want the paradigm to change, but we can't do it on our own, we need the senior people.  I know I have pressure from colleagues and bosses to publish in these journals if I can. Committees for fellowships and future jobs lap these things up, and I'm not in a position to change that.  But Schekman is one of the lucky few who are.

I think on our way up, all of us play the game to some extent.  As long as we know that we're playing the game and doing all we can to change the rules at the same time, I don't think that makes us hypocrites.  We just have to not end up believing in the game if we manage to win it.