News:New Free Community Tutorial Website For Bioinformatics Learning
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9.2 years ago
rob234king ▴ 610

Update

I've updated a static version of the tutorials I put together, see below link (CUBELP2). Note they are for personal use only and are property of the University of Cranfield. I'm talking to my university to approve putting the pdf's on my tutorial sharing website (CUBELP).

Let me know of any recommendations to improve upon them.

Original Post

I've put together a tutorial website with four core comprehensive tutorials on it (feedback needed), RNA-Seq, ChIP-Seq, Genome assembly, and SNP calling.

This website was created to share bioinformatics tutorials and create a dynamic learning environment that does not become dated by allowing the user community to upload and review tutorials in an attempt to create a user learning community. PDF contributions welcome and there are four core tutorials available. I would be interested to get some feedback.

chip-seq snp News rna-seq genome • 7.1k views
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interesting, but why do I need to register before seeing the content ?

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I was wondering the same: C: workflow or tutorial for SNP calling?

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Thanks for the input, I know registering is a bit of a pain but the website is based upon groups that contain tutorials to organise content and I use the login to only show those tutorials from groups you are a member of to make it manageable in the future if it got bigger. You can use false details if your concerned, email etc it's just used for this purpose. If you register it will automatically log you in and if go to "groups" on side bar and join the "Cranfield University" group, then click on "group tutorials" in left side bar you can access the tutorials I have put up. I think they need a little re-formatting but have some useful demonstrations of tools like RSATs etc. Thanks again for the reply appreciate it.

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Have a look at http://www.biotnet.org/

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nice work indeed, but will it contains any video on the future to be more interactive?

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Not as yet as it is my MSc project and I have limited time to develop it. Potentially could add something like that if it became popular, anything which I think provides an additional option that cuts down on the amount of written content to sift through would be advantageous. I'll keep it in mind thanks.

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I must chime in to the criticism, there is nothing on that site now. I would try to come back with an announcement once there is something useful, also I do not see how this site will support e-learning other than providing a space to share pdfs. People are not very patient, so now you might have thrown off a lot of people.

While it might seems a bit awkward I think it is best to close this news for now.

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I figured as much. I've updated a static version of the tutorials I put together, see below link (CUBELP2). Note they are for personal use only and are property of the University of Cranfield. I'm talking to my university to approve putting the pdf's on my tutorial sharing website (CUBELP).

http://elvis.ccc.cranfield.ac.uk/CUBELP2/faces/index.xhtml

Let me know of any recommendations to improve upon them.

Post is closed.

Rob

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Thank you for the update, I found the tutorials under the new link. I will check it out.

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I have updated the top post to reflect the new changes. Great work adding these tutorials.

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9.2 years ago

Basically you have four pdf files hidden under a series of obstacles - such as user registration, then searching for a group then adding that group to yours, then clicking group tutorials then guessing from the title which tutorial contains what one needs.

With those obstacles you just lost 99.9% of the audience that might be interested in your content.

Plus in the end it is not clear what exactly was the point of hiding all that information when the PDFs are large and monolithic. What does the dynamic learning environment actually consist of? Is it a file sharing system where someone could upload a document? Considering that your content are PDFs and are hidden from search engines and you don't offer any search it is difficult to see how this could work at any level beyond the simplest.

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I understand what your saying and if it were limited to those four tutorials I would agree but the aim to go beyond the small university/company led fee paying restrictive practice in which only those who are granted acceptance on a course can learn which is all I could find to help me learn but couldn't get accepted for anything, or really have the money to go. Although that is not to say that these courses are not useful to others but the demand is greater than they currently supply for. If we open up learning to everyone with the aim of covering the whole sphere of bioinformatics. I've posted four very large tutorials on NGS but there is a great deal more than what I have offered in the field of bioinformatics (machine learning etc) and techniques vary. Smaller tutorials may be posted by others. If you click on the play symbol next to the tutorial it opens up a description panel of that tutorial so there is more information on what the tutorial is about other than the title. It's a location for yes "file" sharing in a basic way such as facebook is a forum with a login to share with friends but I see it as a tutorial sharing initiative with an emphasis on reviewing to sift good from bad content. Official run courses become dated quickly, have limited reach, and don't offer the breadth of learning desired by the bioinformatics community. I put this together for these aims in mind and to teach myself NGS and web design as these were not sufficiently taught on my MSc course and I could find little instruction elsewhere.

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Those are all great goals but none of them justifies the attempt to lock away read access. Most of us are trained to think that any site that asks you to register to view content does it for the reasons of being able to take away that right later on or to pull off some other tricks. You would be hard pressed to articulate why a login wall is beneficial to someone that just wants to read a single tutorial, or how that helps any of your stated goals.

It is fine to ask contributors to log in, but not readers, and when you do so you are hurting your own chances for success. I for one would never contribute a tutorial to a site that at any time could take away even my rights to access my own tutorial. I can't imagine an open source contributor that would do so either.

Don't be afraid of free content - whatever your goals are it is very unlikely that you succeed if your first contact with the users is a login wall.

You may or may not agree with this and that is fine, you will soon see that just having a tutorial is not nearly as useful as you think - there is a lot more to bioinformatics than what fits into a PDF, in context discussions and details are essential.

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They are very valid points, I do appreciate your feedback/discussion as an experienced user. I hope I'm not coming across as offensive.

I know people do have a worry about logging in but nowadays everything requires a login to get any kind of experience to a website and are used to it (plus I'm an academic not an employee of the CIA and the website is intended to be for the community). Once you put something online and make it public from what I understand most ownership goes out the door (as long as you reference) unless you charge people for it, login or not. I appreciate it maybe presumes that I am not a shady character however the user can still retain what they have uploaded, I don't delete it off their computers.

If the concept and need which I think are both valid proved true then a superior website could be built from these beginnings, if all it does it highlight the need for something that goes beyond the small courses offered then that would be good.

If I had the programming capability then I would think how to reorganise the website to make it so that you need to login to upload but the group tutorial page uses the login to present the tutorials of every group your a member of rather than all the groups tutorials but then I suppose that could be re-thought. I would also make tutorial submissions displayed at tabs rather than a pdf but only learnt programming this year.

Regarding the discussions and forum, of course essential. Websites like this and seqanswers, and the users there in are invaluable when you become stuck but you need to start in a practical way first.

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Additional: You may prefer a static website of which there are a few and I have also created this for contrasting purposes but it was not the aim of my project to provide four NGS tutorials but a platform to provide the means to share and learn using tutorials within the whole bioinformatics field (which is large).

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9.1 years ago
rob234king ▴ 610

I've updated a static version of the tutorials I put together, see below link (CUBELP2). Note they are for personal use only and are property of the University of Cranfield. I'm talking to my university to approve putting the pdf's on my tutorial sharing website (CUBELP).

http://elvis.misc.cranfield.ac.uk/CUBELP2/

Let me know of any recommendations to improve upon them.

Rob

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that is pretty neat. You should probably create a new and separate announcement on this resource as the main topic of this post is now misleading and the discussions are not that relevant

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9.2 years ago
rob234king ▴ 610

Thanks everyone for taking time to give feedback today. I'm going to remove all the tutorials from the site but keep it running with the hope that it may be of use to the community. I still think the http://elvis.ccc.cranfield.ac.uk/CUBELP/faces/login-page.xhtml can be of some use for the reasons I outlined above however I concede that there is a website that I had not previously heard of http://www.biotnet.org/ with similar functionality, which would be of similar use but at the moment possibly due to lack of marketing and/or community involvement has limited content. Hopefully people will start to contribute and use either the one I have developed or the latter. All the best to everyone on Biostar :)

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