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Anna Croft › Likes
Baking Obsession - Ultimate Mexican Brownies - http://www.bakingobsession.com/2011...
Anna Croft liked this
Can we use game consoles for chemistry? Yes WiiChem - http://baoilleach.blogspot.com/2011...
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Anna Croft and Egon Willighagen liked this
We need an app which shares information between http://www.colwiz.com/ and Papers.app and Mendeley and Endnote and Zotero and Repository
Anna Croft liked this
CRAFT - Chemical Reactivity and Fate Tool | Inspiring Chemical Discovery - http://www.molecular-networks.com/product...
Jean-Claude Bradley and Anna Croft liked this
hmm, based on a very old CDK version it seems
- Rajarshi Guha
Matching results found – a demo of a free online plagiarism checker - http://www.science3point0.com/evomri...
Sebastian Wain, Kubke, Björn Brembs and 2 other people liked this
What happens if I enter the URL of my previous blog post into an online plagiarism checker? Continue reading →
- Daniel Mietchen
I tend to use it at two notches below maximum sensitivity. There are false positives, but these are easy to filter out by eye.
- Matt Hodgkinson
There are also false negatives. For instance, pasting the text **<snip>nachfolgend finden Sie zur Ihrer Information, ggf. auch zum Aushang, einige Hinweise zum nächsten Studienkurs Korea an der Universität Duisburg. Bewerbung für den Studienkurs Korea 2002-2003 Auch im kommenden Studienjahr kann die Universität Duisburg in Zusammenarbeit mit dem Landesspracheninstitut...
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- Daniel Mietchen
Postdoc in my lab available from April 1st. Aiming to demonstrate open source drug discovery, in collaboration with Medicines for Malaria Venture. Really exciting and unusual project. Need someone skilled at synthetic organic chemistry, and who speaks and writes well. Details: https://docs.google.com/documen...
Steve Koch, Mr. Gunn, Anna Croft and 4 other people liked this
Wow, this is moving fast...
- Cameron Neylon
Saw this on orgnet.
- Anna Croft
Comparison of PeerMark and Blackboard Peer Assessment tool - http://drbadgr.wordpress.com/2010...
Cameron Neylon and Anna Croft liked this
Self Assessment and Google presenter - http://drbadgr.wordpress.com/2010...
Cameron Neylon and Anna Croft liked this
Mirza PhD defense on the Ugi reaction for anti-malarial screening - http://www.scivee.tv/node...
Anna Croft and Cameron Neylon liked this
Khalid Baig Mirza defends his Ph.D. thesis at Drexel University on December 6, 2010 (advisor JC Bradley). He first discusses Open Notebook Science and his contribution to the sodium hydride oxidation controversy. Then he describes the UsefulChem project, involving the use of the Ugi reaction as an approach to synthesizing new anti-malarial agents, including a few unexpected side reactions and challenges. Finally he presents an overview of the ONS Solubility Challenge and its application to organic synthesis.
- Jean-Claude Bradley
RT @neilfws: Written any robust, reusable open-source code for your research? We want to publish it - www.openresearchcomputation.com.
Mickey Kosloff, Mr. Gunn, Kaitlin Thaney and 2 other people liked this
Limitless or limited resources. | Indexed - http://thisisindexed.com/2010...
Maureen, Anna Croft, Antony Williams and 13 other people liked this
Thought experiment: Replace "ideas" by some other noun. I just tried "XML", "money", "weapon-grade Plutonium", "jokes" and "problems", and they all still fit into this general depiction.
- Daniel Mietchen
Status update on BJOC analysis with Oscar and ChemicalTagger #2 - http://chem-bla-ics.blogspot.com/2010...
Anna Croft liked this
A shame FF is again missing the images... :(
- Egon Willighagen
Anyone teaching an introductory quantum computing course in the spring? I'm preparing some (free) class materials that you might potentially find useful. If you're interested, leave a comment below, or send me a direct message.
Chris M, Seb Paquet, Clark Kent and 3 other people liked this
(That's very Northern-centric. It's Autumn in the Southern Hemisphere, of course! )
- Michael Nielsen
What about placing those materials at http://wikieducator.org/ or http://en.citizendium.org/wiki... ?
- Daniel Mietchen
Agree with Daniel - Seeing it on those platforms ould be great
- Kubke
The materials are designed for (and integrated with) a special non-wiki platform. It'll become a bit clearer when things are actually done...
- Michael Nielsen
Smartphones wikis and games for education - http://www.slideshare.net/jcbradl...
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Peter Miller, Kubke, Bill Hooker and 7 other people liked this
I think there's something profound embedded in Slide 11, but I can't quite figure it out. X-axis is time / lecture? What's your interpretation of the data?
- Andrew Su
What are the axes?
- Bill Hooker
The downward trending curves are the %attendance vs days from the start of the term. The upward trending curves are RSS subscription numbers. At the end of each term the % attendance was in the 10-20% range but the students who attended vs. those who just watched the lectures online performed statistically the same.
- Jean-Claude Bradley
Interesting... I wonder what those curves would look like if you _didn't_ provide the screencasts... I imagine that attendance drops in most classes. Or said another way, I wonder if you have enough data to segment the performance of non-attenders who did or didn't watch the screencasts.
- Andrew Su
Andrew - I wasn't able to easily identify who watched the lectures and who didn't. When I didn't provide screencasts attendance did drop but not as much - don't have any hard numbers though. Now that I don't repeat lectures and do workshops instead I don't get that curve anymore.
- Jean-Claude Bradley
JC, thanks for the info. I really like the idea. One follow up question. Do you ever get feedback from your students that they miss the interactivity of a traditional lecture? For example, suppose a student has a fundamental question at the very beginning of a lesson. In a lecture they could ask for clarification immediately, whereas viewing a screencast would mean they'd have to wait...
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- Andrew Su
This is fascinating. As a terrible swot who never missed a single lecture in three years' undergrad, I'm astonished at the dropoff in attendance. What was the pattern of repeats -- and what does the curve look like with workshops instead of repeats?
- Bill Hooker
Andrew - the lack of interactivity in the traditional lecture format was a big motivation for me to change. I simply don't have the time to stop lecturing and spend 30 min on a student question if I have to cover a certain amount of material in class. With 4 hours a week of workshops there is time. Some students watch the lectures with headphones during the workshops and pause to ask questions.
- Jean-Claude Bradley
Bill - the attendance with the workshops is very variable. There are spikes before and after tests or when the student hits a particularly difficult patch. For teaching NMR the Spectral Game played in a group works well - for reaction mechanisms (SN1, SN2, etc) the ChemTiles Game is helpful. For other content (like alkyne or alkene chemistry) I find that repeating difficult sections of lectures is sometimes the best option.
- Jean-Claude Bradley
SNP PCR + sequencing workshop at BU- $16 per SNP. Just set up my first sequencing order (yay @Genewiz)! http://twitpic.com/3774tr
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Anna Croft liked this
Great to hear you got it sorted out! Look forward to hearing more on the results. Keep up the good work :)
- Anna Croft
Some more info for my talk at Sydney Uni on Friday including a title and abstract: http://cameronneylon.net/present...
Martin Fenner, Anna Croft, Kaitlin Thaney and 4 other people liked this
Graphing protein databases - http://blog.fuzzierlogic.com/archive...
Piotr Byzia, Anna Croft, Mickey Kosloff and 6 other people liked this
I’m giving a lecture next week to the Bioinformatics Masters students here about protein structure prediction. As part of the introduction to this topic, I have a traditional ‘data explosion’ slide, to illustrate the gap between the quantity of protein sequence data available versus the number of solved protein structures in the PDB (hence the [...]
- Simon Cockell
Nice work!
- joergkurtwegner
RT @F1000: 5 min audio: @CameronNeylon talks about his plans to hack the academic reputation system http://blog.the-scientist.com/2010... #NaturallySelected
Björn Brembs, Anna Croft, Graham Steel and 4 other people liked this
Next time I need to do a protein figure I really am going to learn PyMol properly. This time I mean it...really...[sigh]
Anna Croft liked this
Try here? http://www.bio.ph.ic.ac.uk/~scurry... By no means complete but a useful starter?
- Stephen Curry
Have plundered your quick start guide before which was very useful. In this case I needed to do a homology model, then pick out specific residues and generate pretty picture so multi-step process and I reverted to Swiss-PDB model plus hacking POV-Ray scenes by hand...slow and painful...and then I remembered the reviewer wanted the residues labelled...
- Cameron Neylon
Given that Swiss model generates the worst homology models out there (there was a paper about that 2-3 years ago) and Povray didn't improved its usability much since... 2003 (ca. first time I had used it) I don't think these days you can go much worse than above combination ;).
- Pawel Szczesny
Probably, but its what I know...just wanting to show the position of residues relative to active site...so the model does that job
- Cameron Neylon
But yes, its time I learnt how to do this properly...
- Cameron Neylon
from twhirl
Dear Lazyweb, how do I get a list of genes, ranked according to degree of conservation between two species? Or, how do I get a list of the most conserved genes in sequence-space of any sequenced species?
Carl Boettiger, Christopher Fields, Anna Croft and 5 other people liked this
We're trying to find out if our gene (family) of interest is more or less conserved than any other genes with deep homology.
- Björn Brembs
Ideally gene sequences, but proteins would do if need be. It also finds our gene of interest as #3753 when I compare flies and humans. Interestingly, the human gene it finds is a different gene in the same family compared to a genetic comparison. Is there a way to constrain the search to non-housekeeping genes or transcription factors?
- Björn Brembs
You think someone might be interested? We're in the process of assembling the data for a paper right now and if the sequence data allow us to make the claim that our gene in question is particularly conserved compared to any run-of-the-mill (non-housekeeping-, or transcriptionfactor-)gene, there may be an authorship in there :-) First author is the graduate student who does our PCRs....
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- Björn Brembs
http://biostar.stackexchange.com might help you
- pn
You can constrain the sequence searches to non-housekeeping genes or TFs from sequenced species using gene descriptions or GO annotations. But significant number of genes from most of the sequenced genome still remains unannotated and that will make the annotation based search limited in scope. If you have couple of protein domains of interest, best way is to run a HMMER search using your domains of interest against 'nr' database from NCBI.
- Khader Shameer
Neil, fun graph. Less similarity at high CAIs makes good sense; these are genes that are very well tuned to Drosophila codon usage so will likely either be fly specific or at least have different codon usage in humans. The lower CAI results are less clear. I wonder if this is a sampling bias due to lower numbers of proteins or if there is something interesting about the codon usage at...
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- Brad Chapman
Could this be a statistical distribution? I mean, there seem to be more genes in the medium CAI range and thus the probability that highly conserved genes are among them is higher (similar argument as Brad's).
- Björn Brembs
Would it be possible to highlight certain, known genes of interest in this graph?
- Björn Brembs
Awesome! Would you do that for me? I'd be interested in transcription factors in general (if possible) and this one in particular: http://flybase.org/reports...
- Björn Brembs
There was some recent cool work on something I think is similar by Eric Alm at MIT.
- Anna Croft
@Neil: Hmm, interesting! So it doesn't seem to be particularly conserved when compared to all of the genes. So it would be interesting to carve the genome up along annotations. I agree with forgetting CAI, that doesn't look very helpful, for now.
- Björn Brembs
I know that InParanoid does nice two-way comparisons, but there are a few other databases and methods out there that do multi-way comparisons and list both orthologs, in-paralogs, and co-orthologs. The OrthoMCL database comes to mind, for instance, but I'm not sure how others view it.
- Christopher Fields
Fascinating! Does our gene of interest rank anywhere in particular in the TF group? Are TFs significantly less conserved than the other genes?
- Björn Brembs
The truth…well most of the truth anyway - http://cameronneylon.net/blog...
Anna Croft, Jean-Claude Bradley, Nir London and 8 other people liked this
I had a pretty ropey day today. Failing for 45 minutes to do some simple algebra. Transformation overnight that didn't work...again...and just generally being a bit down what with the whole imploding British science funding situation. But in the midst of this we did one very cool and simple experiment, one that worked, and one that actually has some potentially significant implications. The only things is...I can't tell you about it.
- Cameron Neylon
Yeh, but good to surface it from time to time...just do the check..."yup - this is still a problem...". And the rest of the day was just so entirely shit that it was the kind of thing you want to tell everyone about to cheer yourself up...
- Cameron Neylon
I feel your pain; nothing I do can be in the open for the immediate future, and it grates my cheese something fierce.
- Bill Hooker
I actually find this post refreshing, since it shows that Cameron isn't in some special position where he can happily do open science all the time without resistance, but has to juggle it with old school 'closed' science. It serves as an example that most academic researchers could integrate an open science project or two into their research programs without having to go fully open overnight.
- Andrew Perry
Good point Andrew.
- Pawel Szczesny
from iPhone
Yeh, definitely a good point Andrew. Hadn't thought about it that way.
- Cameron Neylon
I don't think there is a contradiction Cameron - projects (associated with a specific notebook) are ONS not necessarily people.
- Jean-Claude Bradley
No I don't think its necessarily a contradition. Just that I believe we could make much more rapid and interesting progress if we could open it out a bit.
- Cameron Neylon
Cameron can I ask what benefit you get from this particular closed project?
- Jean-Claude Bradley
It's a connection between a project I happen to know about and another one that we're involved in supporting. So I get the warm feeling of connecting two things together, if it does take off we get some big papers and/or patents, and if it gets used and adopted we've achieved our aim of increasing the impact of the facility in general terms. So I guess credit by association with success, which is essentially what I set up as my own criterion for success in the job.
- Cameron Neylon
good luck!
- Jean-Claude Bradley
The real irony of course being the connection was only made by skating around the edges of what should and shouldn't be disclosed...which make the whole process really irritating...which is what sparked the post in the first place.
- Cameron Neylon
Color Survey Results « xkcd (Noting that kernel density functions weren't sufficient for this purpose :) ) - http://blog.xkcd.com/2010...
Anna Croft and Mickey Schafer liked this
Via mkz http://friendfeed.com/mkz...
- Steve Koch
having so much fun delaying work with this -- and great example of how one can use "scholarship" when not having to publish in Nature to keep your job.
- Mickey Schafer
And "dusty" as a modifer is so named b/c it follows "heathered" as a look associated with fabrics. "Dusty" means to have a gray tone, like sage, but applied to any other color in the spectrum. On clothing, this look is very popular and has allowed women to wear pastels without looking like they're dressing for easter and men to wear primary colors without looking like they intend to present health information to kindergartners.
- Mickey Schafer
Color names most disproportionately popular among women: Dusty Teal, Blush Pink. Color names most disproportionately popular among men: Penis, Gay
- Chris Miller
I came across this paper on the gender issue (hosted at another Koch lab :): "This principle of trichromacy is in need of reexamination in view of molecular genetics results suggesting that a substantial percentage of women possess more than three classes of retinal photopigments. [...] Women with four-photopigment genotypes are found to perceive significantly more chromatic appearances...
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- mkz
very cool, mkz!
- Steve Koch
I did a brief literature research but did not find any other papers which would talk about four-chromatic vision (a couple of possible hits were inaccessible to me, though). Any pointers?
- Daniel Mietchen
Daniel, that was the only paper I looked at, but a Google Scholar search returns a few PDF files for human tetrachromacy: http://scholar.google.com/scholar... There are also other species with n-chromacy with n>3. I was surprised to learn that the common jumping spider is one of them: http://en.wikipedia.org/wiki... This guy is even more impressive: http://en.wikipedia.org/wiki...
- mkz
Thanks, mkz - I should have tried it with Latin myself.
- Daniel Mietchen
Do you use (open) electronic lab notebook software? What are you using? I just found the open enventory tool - http://www.chemie.uni-kl.de/forschu...
Imants, Heather Piwowar, Anna Croft and 6 other people liked this
Great. Didn't know about this.
- Matthew Todd
@Matt - Do you know other tools which are getting typically used ?
- joergkurtwegner
This may be of use: http://www.simpy.com/links... (most of the entries are from me -- sennoma was my online nick for years)
- Bill Hooker
Thanks @Bill
- joergkurtwegner
Red-R: A visual programming interface for R - http://www.red-r.org/
Karuppiah Kanagarajadurai, Marcin Wojnarski, Mireille Krier and 21 other people liked this
Hide the code complexity of R behind a easy to interpret visual pipeline.
- Pierre Lindenbaum
Ooh, that looks pretty sweet. I'll definitely try the Linux download when available.
- Michael R. Bernstein
The devs are a pair of graduate students that I know here at BCM. It's a great idea, and I hope it takes off.
- Chris Miller
Looks like Orange and KNIME,
- Abhishek Tiwari
Neil, I understand what you're saying, but I disagree. I'd argue that there are lots of people who do understand the stats but don't have time to learn programming (or the ugly R syntax). They need a one-off analysis done and shouldn't have to call a bioinformatician to do it. Will some people use these tools to do analyses that are just plain wrong? Sure. It's not our job, though, to...
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- Chris Miller
Neil, I uderstand what you're saying. A lot of people confuse learnability with usability. Still, there is usually a lot to be said for making software more usable by a domain expert without making them learn a new set of interface quirks, and for making the necessary domain complexity available, and accessible, without forcing the user to stare at it all the time.
- Michael R. Bernstein
"Save both data and analysis into a single file and share."
- Andrew Lang
Similar idea of a pipeline is in Debellor (for Java) - www.debellor.org - but without this nice GUI, yet. The advantage of Debellor is that data can be processed really in a pipeline/stream, i.e. sample-by-sample, not by whole table at once, so scalable computing with massive data is possible no matter how much RAM you've got installed
- Marcin Wojnarski
NMR integration web service expanded - http://usefulchem.blogspot.com/2010...
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Anna Croft, Brian Westra and Andrew Lang liked this
How can I make a graph that looks like this, "tweet density" style, showing time intervals? I have a static data set, so it doesn't need to be fancy.
Pierre Lindenbaum, Anna Croft, Burak Kutlu and 4 other people liked this
My data is in csv format (time started, time finished, date) and I'm most familiar with Excel, but sample R code would be OK too. I'd prefer something I can do locally, without installing PHP and a bunch of scripts or graphics libraries.
- Mr. Gunn
What I like about the above visualization is that it simplifies data like a histogram but shows trends over time, too.
- Mr. Gunn
Something similar could be done in Excel by splicing together a bar chart from each day.
- Mike Chelen
I asked @tweetstats about it and he told me it's just Gantt chart, so I'm whacking something together as we speak.
- Mr. Gunn
Yup, @TweetStats guy here. You can see the template I used on the bottom left of this page - http://www.fusioncharts.com/free... - I just modified the height/opacity of the bars relative to the frequency of tweets on each day/hour.
- Damon Cortesi
XML source of the chart is available here - http://tweetstats.com/cache... (replace dacort with your own screen name to see yours)
- Damon Cortesi
Thanks bunches!
- Mr. Gunn
One day I will be able to proudly say that I had actually met Damon when he was still a security guy :)
- Deepak Singh
Hmm...having trouble representing more than one time series in a given day. Probably going to mess with this more later.
- Mr. Gunn
Wow, thanks, Neil. I'm definitely going to steal this.
- Mr. Gunn
Anna Croft and Jamie McQuay liked this
The importance of stupidity in scientific research http://jcs.biologists.org/cgi...
Steve Koch, Dan Hagon and Anna Croft liked this
Sleepy-Time Tips for Extreme Multitaskers - http://www.wired.com/underwi...
Björn Brembs and Anna Croft liked this
So funny. So true.
- AJCann
from Bookmarklet
openchemistry | Openchemistry makes chemistry learning content free, open and available to the world. - http://openchemistry.co.uk/
Marie, Jean-Claude Bradley, Paul Bacchus and 6 other people liked this
"The purpose of OpenChemistry is to make chemistry learning content free, open and available to the world with the aim of creating a community of educators, students and lifetime learners who are interested in producing and consuming original content in chemistry All work by openchemistry is licensed under a Creative Commons Attribution 3.0 United States License, which means that you are free to use and modify it for any purpose. All we ask is that you include a link back to openchemistry in your credits."
- Mackenzie Cowell
from Bookmarklet
Although there seems to be a spam entry on Tue first page that has been there since August...
- Cameron Neylon
from Android
looks like my lectures are still there :) http://openchemistry.co.uk/...
- Jean-Claude Bradley
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