Collaboration: bringing NN members together: topic
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Bob O'Hara
Friday, 28 March 2008 07:26 UTC
Just to get things started, here’s a place to say what sort of collaborations you’re prepared to engage in, how much time you have free to spend etc. And if you have any particular problems that you want help with.
It is also worth checking other fora and groups, particularly is you have “small” questions that you need help with. For example, if you can’t figure out what sort of analysis you need for a particular problem, hop over to the statistics group.
Updated 28 March 2008 07:38 UTC
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Well, I might as well start. I’m a statistician, so I’m interested in collaborating on data analysis. Mainly in ecology and evolutionary biology, but I don’t mind going wider. As long as it’s interesting.
Of course, I have far too much to do anyway, so a couple of extra small projects won’t do any significant harm!
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This will be the group mantra: “I have far too much to do anyway, so a couple of extra small projects won’t do any significant harm!”
I can help out with questions relating to developmental roles of your favorite gene.
I also run a cottage industry in interpreting histological sections or any odd knobs and bumps of any vertebrate embryo you might want to submit.
I’m good at telling when it will be too much for me and putting you in contact with someone else, instead.
What I get out of it: practice in time management and meeting folks in other fields.
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I’m a bioinformatician and I would enjoy to be of any help for a small project (database, graphical tools,...).
“I have far too much to do anyway, so a couple of extra small projects won’t do any significant harm!” :-)
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I’m in industry, working for Gene Tools LLC. We make Morpholino oligos. I offer advice or discussion about antisense projects.
Rarely I can also contribute a few free Morpholino oligos to a project. For that, the project must potentially open a new market for Morpholinos. As an example, I collaborated with Wigard Kloosterman while he was a doctoral student at the Hubrecht lab to use Morpholinos to inhibit activity and maturation of miRNAs in zebrafish, an application that has since become popular. If your project has a good chance of leading to significant Morpholino orders from other groups later (orders which would not have occurred without the initial project), there is a chance that I can have some collaboration oligos made for you.
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I can help with Bioinformatics. Or Evolution. Or Phylogenetics. Tips and tricks, analysis ideas, small projects, you name it.
I have a blog about learning Python for bioinformatics and if you have any issue or subject that you want covered, just let me know and I write about it.
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I’m good at pies and beer.
Oh, and professionally, I’m a bit of a jack of all trades. Cell biologist cum mol biologist cum structural biologist cum the ‘Ned Kelly’ of bioinformatics.
I’m an inveterate tool stealer. Whatever it takes, ma’am.
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I’ve worked in bioinformatics and computational biology since 2000. Before that, I spent 6 years in various labs doing biochemistry, molecular biology and microbiology. So if you’re a biologist asking advice on a computational problem, you don’t have to explain what DNA is to me :)
To me, all biology is information. My particular focus for several years was microbial genomes, but I don’t mind if you work on crystallography, cancer, yeast, fruit flies, wilderbeest or whatever. We’re all in the business of information: generating it, storing it, analysing it and presenting it – academic subdisciplines and fields are irrelevant.
The best place to find out what I do is probably my blog. My daily activities can be followed at multiple social networks.
I’m something of a “jack of all trades” bioinformatician, so I can handle most types of data that you may want to throw my way. My particular skill is taking large datasets (sequences, structures, genomes), filtering them: “show me all the proteins with features XYZ” and presenting the results in a useable way. Many such problems can be solved using the BioPerl libraries and a few lines of code.
I’m a big fan of web social networks and an advocate for free, open-source software. If you’re looking for an educational resource on the web or an alternative to your current software, I can probably point you to the right place. I’ve used Linux as my sole OS at home and work for about 6 years.
Time constraints: I’m reasonably independent but I am a postdoc answering to a group leader, so I have those obligations. I’m happy whipping up quick scripts (a few hours work) for people. Anything more than that becomes “genuine collaboration” and requires that (1) I find your work really interesting and (2) my contribution be recognised appropriately, i.e. co-authorship. If I don’t have time for your project, I’ll tell you straight off (rather than half-starting, then backing out…) and point you to whatever resources might help you out. One such place is Nodalpoint, where you’ll find more people willing to answer questions.
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I’m a cancer researcher working in a university hospital. My research interests are testicular cancer, malignant bone diseases and nuclear hormone receptors in cancer. I can help out with clinical samples and clinical data in these diseases.
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I’ve got a background in protein chemistry, biophysics, and high throughput methods development. More recently I’ve been focussed on developing tools and approaches for enabling open science and more particularly Open Notebook Science, where we make our lab books immediately available to the outside world.
In terms of collaborations my group has a few tools in search of a problem (or at least someone who wants to apply them to a problem). We are pretty good at selective labelling of proteins at the C-terminus using Sortase mediated ligation. This works for putting a single fluorophore, small molecule, piece of DNA, or solid support gently, cleanly, and covalently onto the protein. Happy to help people out with that. We have expression vectors and such like available.
We have a few screening assays which we could use for testing compounds against Sortase (S. aureus drug target) and HIV protease. We’ve developed other assays in the past. These can be costly and time consuming to run but for small numbers of compounds it should be possible to find time.
As part of a project on high throughput DNA sequencing I was involved in the development of some computational tools for identifying sequence repeats in strings and visualising the repeat structures identified. If anyone needs tools of this then give me a yell and we’ll see whether we can help you.
And if anyone is interested in making more of their data and protocols available to others but aren’t sure how to go about it then I’m very happy to help with that.
Finding time to get things done is tough but am happy to work with people to develop collaborations and have a fair amount of latitude as to what my science priorities are.
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Like Richard, I’m good at pies and beer but also Kung Foo Cooking.
That aside, I’m a layman currently interested in Protein Misfolding Diseases (PMD) and the diagnosis and treatment options thereof.
I am especially interested in Glycobiology
I like to build on the past in creative ways.
For more info/background, check out my recent interview with Bora Zivkovic.
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