Where the hell is the future of ANT+ ?
Where's the open standard, not owned and squirreled away by Garmin?
Where's the fiercesomely forward thinking Ergo that links wirelessly an iPhone to a HR meter? Where's the ConceptIII iPhone app?
Where's the brass monkey balls to get a damned HR monitor out to the public?
Fitbit is just a hint of what tech could actually do.
And then it might actually be damned useful, rather than just damned late.
Tuesday, 15 December 2009
Thursday, 23 July 2009
Augmented Reality and dance
Lightstage - need to email to see what's happening.
Project Natal is in concept, a one sided version of this.
Presumably the next stage is to make Natal comprehend multiple angles. Rig a few cameras up in different corners of the room, and then all sidess are seen.
Mocap for the 21st century.
Head cam for the 21st century: http://gizmodo.com/5320375/christian-bale-rant-victim-is-the-man-behind-the-canon-eos-5d-mark-ii-helmet
Why?
This can capture a dance, both in video, but also in 3 Dimensional space, showing your body movements (at least at the simple level, but presumably start to get more refined and higher resolution).
- Your dance
- Your teacher's dance
- A dance at an event
- A private lesson
- At a dance hall
Recall - you have the dance captured - you can go over fine detail whenever, wherever
Improve - you can problem solve spins, movements, timing (care to have the 3d visually pulse with colour in time with the music beat/rhythm/instrument)
Learn - See a routine and slow it down - at a much finer level and smoother when at non-1x speeds.
Could you have 2 streams of data - a HD or VGA version, and then along that the feed from what the Natal webcam receives as input/ what gets crunched and uses as output. If you could collect both at the same time, close enough, you could even overlay them - in in effect add motion capture skeletons, avatars overlaid or whathave you.
Whether or not this is Real Time (RT) - in effect you get to a wirestick model of people, with avatar possibilities.
A move library, where every move could smoothly be linked to every other one?
Think this needs pictures.
iPhone App 2 Salsa learning
If Mental Case got n-sided cards (so you could have a card for footwork, card for key points, card for what it linked from and linked to in a routine (or what it could link to/from). That'd be useful - Drew's already talking about audio, and possibly video.
With video, you could link snippets of a routine - literally splice out each move, to then allow (you'd have to line up the camera for the start and end positions :/) you to mix and mtch moves to make a routine, or video a routine, splice, then remember it/ what your routine form different classes could be like joined together in various ways (so the video pieces being say x number of bars long rather than just 2-4).
With video, you could link snippets of a routine - literally splice out each move, to then allow (you'd have to line up the camera for the start and end positions :/) you to mix and mtch moves to make a routine, or video a routine, splice, then remember it/ what your routine form different classes could be like joined together in various ways (so the video pieces being say x number of bars long rather than just 2-4).
iPhone App 1 Salsa
An example of what Google Maps can do - mapping extreme sports locations on a map.
But a pin in a map doesn't help so much, as a rank by wind/distance/quality of sites, knowing where you are and how far it is to drive to the locations - all info you can gather and push to the user.
Same with salsa - there are several static lists of events and classes, that get updated at various speeds - but you've got to search through most - a list of addressses.
With decent data on each venue - when where, level, how much, who by, parking info, how long, what style etc
You could start to move away from a nasty excel spreadsheet, and more towards a more useful UI for a person looking to go and have a dance, or a dance lesson, whereever, whenever.
But a pin in a map doesn't help so much, as a rank by wind/distance/quality of sites, knowing where you are and how far it is to drive to the locations - all info you can gather and push to the user.
Same with salsa - there are several static lists of events and classes, that get updated at various speeds - but you've got to search through most - a list of addressses.
With decent data on each venue - when where, level, how much, who by, parking info, how long, what style etc
You could start to move away from a nasty excel spreadsheet, and more towards a more useful UI for a person looking to go and have a dance, or a dance lesson, whereever, whenever.
Friday, 19 June 2009
Your new phone, and how to improve your dancing
I think a few of you might want to go get an iPhone 3GS.
Or maybe not. Stephen Fry would recommend them - "for the moment however, no one can deny that with the iPhone 3GS the gold standard has been set."
This post is to highlight the possible benefits, if you had one, and you wanted to use it in conjunction with your salsa dancing.
So the question on a salsero's or salsera's lips could be - is it useful for Salsa? Well possibly. The only drawback is the price. Can you afford it? And can you afford to take it out dancing? If you can answer yes to both of those then you have certain benefits:
Video
The video quality on the iPhone 3GS is VGA 640x480 30 frames per second - better than small youtube video quality. It does autofocus photographs, auto-light balance, and handles panning and motion fairly well (with the option to correct for motion shakiness afterwards through software on a computer). It's not Flip quality, but it does seem to suffere less distortion when panning it seems.
What does that look like? Here's a quick video, recording a youtube video to show you rough quality. Bear in mind that youtube actually compresses the actual recorded video.
You do a lesson, and then record the final runthrough demonstration, and then you've got that reminder video stored on your phone. You can share it, you can edit it, whatever.
There is great power to be able to archive lesson patterns, or insights, thoughts, or even just video your friends for feedback/encouragement/to show them how good they are. I know that Anthony at addicted2salsa has mentioned the iPhone before in several contexts (Shazam app to identify music, photos, storing a2s videos! Being his precious...)
Storing a back catalogue of audio & video podcasts
There is a decent amount of salsa on iTunes - e.g. Addicted2Salsa's HD video podcast - link to subscribe in iTunes here. That looks great on the iPhone, and iPod Touch.
I'll add the unlikely salsero link if I can find it. (Edit - this one and this one I think).
SatNav
It does decent GPS based Google Maps guidance to an event, with the option to get a TomTom application and charger/holder soon. Info here -
GPS
This is so cool, I'd watch the Engadget review here In particular, this video. You won't get lost.
Camera
The best camera, is the one you have with you. There are better picture taking phones out there. But, bear in mind, that the iPhone is the most popular handset model to upload pictures to Flickr for example - it's so easy to email, post to Flickr, MMS, or blog about pictures you've taken. It does good pictures, for a 3Megapixel camera. No camera flash here, but it's good.
Email, SMS
No more waiting, you can be being productive whilst you wait for your friends to arrive, and you can keep in touch with them
There will be more reasons, but for now, these are the ones off the top of my head!
For some more ideas about the video, have a look at this gallery here
Guided tour of the iPhone 3GS
More salsa posts here and some previous thoughts on an iPhone app.
Saturday, 13 June 2009
Gary Vee needs an iPhone app
Seriously - wine buying needs to get much improved, and the G2/ iPhone 3GS could help with this.
Google has the tech to warp a distorted image to a straight image (used in their book scanning project, but a company could do something similar, as wine bottles pretty much have a simimlar shape where the label is, and they usually have straight edges, or at least the text is in horizontal lines...)
So what do you need?
Which shop? ID the location with the GPS / select supermarket, then a list of the supermarkets.
Which wines? Select what you want - price range, type (white red bubbly dessert)
Then the painful database bit - trying to display some wines the shop has. Now the supermarkets now this detail, but they won't likely let no what's on the shelves - but the churn isn't going to be that big - many supermarkets will have similar stock. Once the base stock for a small, medium and large supermarket is identified (crowd source!) then it's just updates to stock, and price changes/ offers.
Wish Gluck had been round for this kind of thing. Now this would be very mucheasier for supermarkets, but their concern is linking easily a review of a wine to their stock - it very easily identifies how good the wines they stock are, and also value for money.
In relation to http://en.wikipedia.org/wiki/The_Cluetrain_Manifesto -
Google has the tech to warp a distorted image to a straight image (used in their book scanning project, but a company could do something similar, as wine bottles pretty much have a simimlar shape where the label is, and they usually have straight edges, or at least the text is in horizontal lines...)
So what do you need?
Which shop? ID the location with the GPS / select supermarket, then a list of the supermarkets.
Which wines? Select what you want - price range, type (white red bubbly dessert)
Then the painful database bit - trying to display some wines the shop has. Now the supermarkets now this detail, but they won't likely let no what's on the shelves - but the churn isn't going to be that big - many supermarkets will have similar stock. Once the base stock for a small, medium and large supermarket is identified (crowd source!) then it's just updates to stock, and price changes/ offers.
Wish Gluck had been round for this kind of thing. Now this would be very mucheasier for supermarkets, but their concern is linking easily a review of a wine to their stock - it very easily identifies how good the wines they stock are, and also value for money.
In relation to http://en.wikipedia.org/wiki/The_Cluetrain_Manifesto -
Thursday, 11 June 2009
iPhone 3GS - Game changer for the blind and the nagationally challenged?
Listening to TWiT Live's repeat showing of MacBreak Weekly, episode 144 - they joked about the feature of maps and a digital compass.
But what if you took 3D audio, and then knowing the direction of the phone, and then a map, you could provide a touch screen app that would give street names around you in 3D audio space as well as visually. You could get it to give info about upcoming road junctions.
For the blind, they could plug in their iPhone, and then if they wanted to find a store, go into Voice control Google search, then route a route, then follow audio directions, along with a guide dog/walking cane.
For those with sight, but not a good sense of direction and orienteering, it could also be used to train people up on the skills needed.
They joked if you could put glasses on and make it across town without looking anytime. But that's what a blind person I guess does every day...
Wonder where you can find up to date info on tech for the blind.
Wednesday, 20 May 2009
Masters project
Currently in the writing stage for Section I - the Introduction and Background section.
THe project is about the potential to find out where amino acids could bind to a ligand, and then build a receptor's CDRs from there- using a known framework to link them, not bothering too much about buildiing the whole damn thing, just getting key amino acids in roughly the right position, relying on flexibility and induced fit to help out.
THe project is about the potential to find out where amino acids could bind to a ligand, and then build a receptor's CDRs from there- using a known framework to link them, not bothering too much about buildiing the whole damn thing, just getting key amino acids in roughly the right position, relying on flexibility and induced fit to help out.
Thursday, 14 May 2009
Accessory market for Apple's iPhone and Touch
This is speculation, pure and simple.
WWDC 2009
For WWDC I see a number of things. Apple could have got China on board. A new iPhone with IMG POWERVR multicore chips if we're lucky.
I also see
- A new dock
- Lots of accessories. If WWDC 08 was apps, WWDC 09 will be accessories
This will create a big bow wave of consumer demand, and a large wake.
The accessory group is shrouded, and rightly so. The ADC has been infiltrated by some folk just there for the beta OS, and to poke around. Hence in all likelihood Apple creating it's own high end ADC forum on Snow Leopard, for those with the money, and possible disdain of riff raff!
IMG is looking to be getting close to Apple. IMG's already talking about OpenCL -and they're hiring OpenCL positions. Seeing as a high up from IMG basically said multicore IMG POWERVR in a mobile at latest by May 2010, either v3 or a v4 iPhone is going to get OpenCL on it.
Which means that Snow Leopard tech *is* coming to iPhone OS. iPhone OS will be 10.6 derived, not 10.5
I can bark up lots of wrong trees - but the possibilties that Imagination Technologies is linked to Toumaz Tech - who do sensors - and that Apple's involved?
Blimey. If they were doing a Tablet, to push to the medical field - then these kinds of companies and deals would give them medically certified applications and also sensors. From Blood Glucose (ain't just Johnson and Johnson doing it then!) monitoring to sport.
Horseracing. Football.
That dock - See Erica's ars Technica posts - basically Apple will have a dock, as per the Media Out Interface patent, that will allow an iPhone to video out HD gaming screen whilst playing, or show a HD film / video onto a HDTV with ease.
The upgrade to the cables is to do with this, i'm darn certain.
http://www.theiphoneblog.com/2008/12/08/play-moto-chaser-iphone-tv/
http://www.youtube.com/watch?v=qwQPNSt-CF0&fmt=18
What's the hassle of showing video you've made? Quite a bit. This really opens things up.
You record on the iPhone, edit on it, upload onto MobileMe *Aand* you also get to show it off to anyone with a TV.
Yes, some of this is done before, but not with the potential level of integration I believe we're going to see.
There's already an unpublished API on this - so Erica could put a game onto a TV.
This is a pincer movement invasion of the living room from a handheld mobile device, that is also a phone.
A possible app.
But I'm seeing this in good old sculling, for my father bless him. At some point over the summer, the new coding project is to create a modular app for him so he can take an iPhone out sculling,
and have features that help him.
In rowing - you're facing backwards. It's like reversing a car faster than you can ride a bike, faster than you can jog or perhaps run.
The tech to see behind , rather than have to twist the neck every couple of strokes (bearing in mind that for every stroke you've covered 10 metres or more, so you'll have covered the length of a football pitch in 9-12 strokes.
And there are bloody big metal/plastic bouys, banks, Saga-laden ferries, boats and other scullers all inthe mix too.
So that's the new project. I'm seeing a big Sports push in the accessory tech market with iPhone and Touch. And I don't see too many people fleshing it out as much as I think it could run.
Even the damned dock coming in WWDC to join the iPHone to the HDTV is immense - in one accessory, Apple's just taken over the living room.
iPhone with cable to TV/dock to HDTV
or iPhone wireless to dock/ATV to HDTV.
Have you got broadband and a TV? Then you're set to download HD film rentals, through Apple's iTunes ,and watch through the iPhone.
Massive win.
Thursday, 7 May 2009
Sunday, 5 April 2009
Voice recognition, on a future iPhone?
How much power would it need, if it were to delegate the learning to it's syncing computer?
Nuance owns:
T9 text input (Tegic - AOL owned for a while, but somehow went to Nuance)
Dragon Naturally Speaking (Wond a best of show at MWSF 2008)
And has it's foot in the medical secretarial door.
System requirements:
System Requirements
Audiomining http://www.nuance.com/naturallyspeaking/products/sdk/sdk_audiomining.asp
http://news.bbc.co.uk/1/hi/technology/7982763.stm
You'd need it open source - and ubiquitous . Seeing as you talk a lot on the phone, you'd be uniquely able to get a decent recording of key words in training, and modifier samples if you say something uniquely, through recording one side of the conversation.
Probably an ethical nightmare, but you could always upload a profile made on a desktop/laptop - or even do the 15 minute speech on the phone and then email to get analysed.
Nuance owns:
T9 text input (Tegic - AOL owned for a while, but somehow went to Nuance)
Dragon Naturally Speaking (Wond a best of show at MWSF 2008)
And has it's foot in the medical secretarial door.
System requirements:
System Requirements
- Intel-based Mac
- Max OS X 10.5.1 or greater ("Leopard")
- Internet connection required for product registration
- 2GB of free hard drive space
- A MacSpeech-certified USB noise-canceling microphone
Audiomining http://www.nuance.com/naturallyspeaking/products/sdk/sdk_audiomining.asp
http://news.bbc.co.uk/1/hi/technology/7982763.stm
You'd need it open source - and ubiquitous . Seeing as you talk a lot on the phone, you'd be uniquely able to get a decent recording of key words in training, and modifier samples if you say something uniquely, through recording one side of the conversation.
Probably an ethical nightmare, but you could always upload a profile made on a desktop/laptop - or even do the 15 minute speech on the phone and then email to get analysed.
Monday, 16 March 2009
The tweeting dancers
A top 100 dancing twitters:
Can we reach a 100 tweeting dancers?
Are you a dancing twitter user and want to join the list? Tweet me, add a comment here, follow me, or retweet http://bit.ly/danceontwitter - I'll add your website link, bio and/or info.
(Thanks for sciencebase for the idea, with http://bit.ly/scientwists which has gone from 100 to >200 folk on the list!)
This may evolve - It really needs to be a drop down table, to give user chioce of what to rank by
Alternatively, just check out the following list for the big dance players on twitter :)
Can we reach a 100 tweeting dancers?
Are you a dancing twitter user and want to join the list? Tweet me, add a comment here, follow me, or retweet http://bit.ly/danceontwitter - I'll add your website link, bio and/or info.
(Thanks for sciencebase for the idea, with http://bit.ly/scientwists which has gone from 100 to >200 folk on the list!)
This may evolve - It really needs to be a drop down table, to give user chioce of what to rank by
| Screen Name | Twitter Bio / Info | Website | |
| addicted2salsa | Anthony Persaud of addicted2salsa fame - Check out his free HD salsa videos on iTunes, and forum | addicted2salsa.com | |
| danceadvantage | Dancer, dance teacher, choreographer, writer, mommy | ||
| danceinisrael | English language resource about dance in Israel (Deborah Friedes) | http://www.danceinisrael.com/ | |
| dancetherapy | dancetherapystudios.com | ||
| movmnt | Fashion, Dance, Music & Pop Culture Together as a Lifestyle | http://www.movmnt.com/ | |
| RitmoBello | RitmoBello - | ritmobello.com | |
| salsacrazy | Evan from salsacrazy.com | salsacrazy.com | |
| sydneyskybetter | Choreographer | http://www.skybetter.org/ | |
| tendutv | Broadband network featuring concert dance and screendance | http://blog.tendu.tv | |
| t0mat0 | futuresoundings.blogspot.com | ||
| You! | Your info! | Your website! |
Alternatively, just check out the following list for the big dance players on twitter :)
Sunday, 1 March 2009
Bioinformatics Software Engineering Group Project
We got our group project brief last Tuesday, with our 1st meeting with the "clients" last Thursday.
The brief:
CRIC has asked for us to create a prototype web-based application to tender for a contract to create a full program. Our "company" (our group) needs to demonstrate this working prototype in 3 weeks (so we can hypothetically "win" the contract, and design the program).
Specification:
Papers Download
• Enable users with means to retrieve online research papers using a search term. The system should query against online resources (e.g. Direct Connect, Wiley International, Google Scholar and Web of Knowledge) using appropriate passwords from user (or could be retrieved from database) and attempt to search for and download selected papers. Allow for other services in the future.
• If full papers are not available, at least the abstract and publication information should be downloaded.
- Scopus, other resources that work are feasible alternatives. No preference with resource, but want something working for the prototype
2. Search for gene and/or protein IDs
• The web application should provide the user with means of retrieving genes and proteins information using a search term (e.g. Breast cancer).
• The system should give the user the flexibility to specify the online resources he wants to query, the following bioinformatics resources are of particular interest to our researchers at the moment – these may change: Ensembl (EBI), Swiss-Prot/Uni-Prot, Entrez (NCBI),
Protein DataBank (PDB).
• The user should be kept informed of the results retrieval process.
3. Upload and analyze custom datasets
• The system should also give the user the possibility to upload custom dataset files. Once uploaded the user should be able to assign privileges for browsing, modifying, downloading the dataset by:
i)only the user, ii) the user workgroup, iii) everyone
• The developed system should also support the integration of data analysis plugins. For the purpose of this prototype, you can adopt one or more of the data analysis scripts you have developed throughout the year (e.g. sample data and analysis script from Module 1 and/or
Module 5 assignments) and make it excutable through the web application.
• You are required to choose a model dataset to test your analysis script. This can be any datasets that we have been provided with. The dataset & analysis scripts you decided to implement will be discussed during one of the early meetings with the client.
• Modularity of the associated analysis scripts should be well respected. A detailed section describing methodologies for adding more analysis scripts should be provided with the written report.
4. Local Database
• Design a database schema to store all relevant collected information using appropriate keying and indexing.
• User login details, online search results, links to the uploaded datasets, as well as data analysis output should be stored and managed within the database
- Registration system, manage the users and their data.
- Registered users should be able to login to his own space on the system (think of msn or facebook space), to manage and store his experimental results.
- The system should also provide different levels of security for the stored/retrieved data.
So we need to sort out, amongst other things
- the userspace (registration, log in, sessions, linking the user to their data)
- the permissions/security (personal, group and public settings)
- 1, 2, and 3.
We have Netbeans, MySQL, R and anything free to use to implement pretty much. We can add bits, hack things in, as long as we reference.
If you were to do this project, what solution might you take for this?
What do you think might be the things that take the longest time?
Some helpful pointers would be welcome, and hopefully I can update on how it's going if anyone would be interested.
The brief:
CRIC has asked for us to create a prototype web-based application to tender for a contract to create a full program. Our "company" (our group) needs to demonstrate this working prototype in 3 weeks (so we can hypothetically "win" the contract, and design the program).
Specification:
Papers Download
• Enable users with means to retrieve online research papers using a search term. The system should query against online resources (e.g. Direct Connect, Wiley International, Google Scholar and Web of Knowledge) using appropriate passwords from user (or could be retrieved from database) and attempt to search for and download selected papers. Allow for other services in the future.
• If full papers are not available, at least the abstract and publication information should be downloaded.
- Scopus, other resources that work are feasible alternatives. No preference with resource, but want something working for the prototype
2. Search for gene and/or protein IDs
• The web application should provide the user with means of retrieving genes and proteins information using a search term (e.g. Breast cancer).
• The system should give the user the flexibility to specify the online resources he wants to query, the following bioinformatics resources are of particular interest to our researchers at the moment – these may change: Ensembl (EBI), Swiss-Prot/Uni-Prot, Entrez (NCBI),
Protein DataBank (PDB).
• The user should be kept informed of the results retrieval process.
3. Upload and analyze custom datasets
• The system should also give the user the possibility to upload custom dataset files. Once uploaded the user should be able to assign privileges for browsing, modifying, downloading the dataset by:
i)only the user, ii) the user workgroup, iii) everyone
• The developed system should also support the integration of data analysis plugins. For the purpose of this prototype, you can adopt one or more of the data analysis scripts you have developed throughout the year (e.g. sample data and analysis script from Module 1 and/or
Module 5 assignments) and make it excutable through the web application.
• You are required to choose a model dataset to test your analysis script. This can be any datasets that we have been provided with. The dataset & analysis scripts you decided to implement will be discussed during one of the early meetings with the client.
• Modularity of the associated analysis scripts should be well respected. A detailed section describing methodologies for adding more analysis scripts should be provided with the written report.
4. Local Database
• Design a database schema to store all relevant collected information using appropriate keying and indexing.
• User login details, online search results, links to the uploaded datasets, as well as data analysis output should be stored and managed within the database
- Registration system, manage the users and their data.
- Registered users should be able to login to his own space on the system (think of msn or facebook space), to manage and store his experimental results.
- The system should also provide different levels of security for the stored/retrieved data.
So we need to sort out, amongst other things
- the userspace (registration, log in, sessions, linking the user to their data)
- the permissions/security (personal, group and public settings)
- 1, 2, and 3.
We have Netbeans, MySQL, R and anything free to use to implement pretty much. We can add bits, hack things in, as long as we reference.
If you were to do this project, what solution might you take for this?
What do you think might be the things that take the longest time?
Some helpful pointers would be welcome, and hopefully I can update on how it's going if anyone would be interested.
Thursday, 12 February 2009
Cytoscape
Diversion. An interesting product, and am curious as to whether on the side you could use it for some rough and simple social network analysis:
You can get the ID of your twitter followers and who you're following in XML format, strip the format, then use to find these folks followers and who they're following.
the useful part would be to add a filter, to be able to check to see if they had at least one post with a key word in, e.g. bioinformatics, or Ruby or RoR. To pare down the graph a bit, as i'd suspect it would get horrendous after a few links deep.
http://apiwiki.twitter.com/REST-API-Documentation#SocialGraphMethods
http://yoan.dosimple.ch/blog/2007/05/17/
http://flowingdata.com/2008/03/12/17-ways-to-visualize-the-twitter-universe/
http://www.tweetwheel.com/YOURUSERNAME
http://www.orgnet.com/twitter.html
You can get the ID of your twitter followers and who you're following in XML format, strip the format, then use to find these folks followers and who they're following.
the useful part would be to add a filter, to be able to check to see if they had at least one post with a key word in, e.g. bioinformatics, or Ruby or RoR. To pare down the graph a bit, as i'd suspect it would get horrendous after a few links deep.
http://apiwiki.twitter.com/REST-API-Documentation#SocialGraphMethods
http://yoan.dosimple.ch/blog/2007/05/17/
http://flowingdata.com/2008/03/12/17-ways-to-visualize-the-twitter-universe/
http://www.tweetwheel.com/YOURUSERNAME
http://www.orgnet.com/twitter.html
Wednesday, 11 February 2009
Could you help with a Perl project?
I was wondering if anyone might be able to help a bit, with a current Perl based project i'm working on. Given some peptide fragments from Mass Spec experiments, including duplicate epxeriments on the same protein, and given the gene ID, looking to compare the found peptieds, with what wasn't picked up by Mass Spec, that should have been created by trypsin digest, and potentially shown through MS.
Given a text file with the structure
>GENEID1
PEPTIDE1, PEPTIDE2, PEPTIDE3
e.g.
Any pointers? Or an idea through some pseudocode? I can update post and include code so far.
I can use BioPerl pepstat, emows etc I'd imagine. Or collate the physicochemical properties in an array and then export to R, but i'm happy to just get figures, then do visual analysis/ some data chewing through Perl's graph tools.
Given a text file with the structure
>GENEID1
PEPTIDE1, PEPTIDE2, PEPTIDE3
e.g.
>ENSG00000000971Looking to create perl script to determine the properties of these 2 groups - the observed peptides, and the unseen peptides. Then compare the properties of the two groups (isoelectric point, length, MW, amino acid composition etc).
ISEENETTCYMGK,SEENETTCYMGK,EENETTCYMGK,PPQIEHGTINSSR,PCSQPPQIEHGTINSSR,QPPQIEHGTINSSR,PQIEHGTINSSR
>ENSG00000005421
VTQVYAENGTVLQGSTVASVYK
Looking to analyses this. To compare the "seen" peptides, with the "unseen" peptides, e..g physicochemical properties.
Wondering what properties might make certain peptides observable, others not so.
Any pointers? Or an idea through some pseudocode? I can update post and include code so far.
I can use BioPerl pepstat, emows etc I'd imagine. Or collate the physicochemical properties in an array and then export to R, but i'm happy to just get figures, then do visual analysis/ some data chewing through Perl's graph tools.
Wednesday, 4 February 2009
But first, some Phylogenetics
Happily getting in outside speakers on our course, a recent one was on Phylogenetics, given ably by Julia from GSK,QSci on 27th January. The date is important in part, because the New Scientist had this cover and story for the 21st. No mention of it in the lecture, but it does throw up some points.
"Darwin was wrong". The full article is here
Phylogenetics: what, how and when
So i'm listening and watching the presentation, and reading the article at the same time, and it felt at the time that more skepticism was needed. It's sometimes hard to gauge if the speaker means it when they say they'd like questions even during the talk. I'm all for asking questions, up to the point my coursemates get annoyed, and I get close to asking too many.
So go read the article linked above - The picture in the articke is close to that used in the 1st main slide, regarding "Phylogeny -a brief history" (which stated "the display of inferred relationships as a tree can be traced back to Charles Darwin) So that's inferred relationships. This is a model. There is no spoon.
The brief history covered the
1960s
- Origin of molecular biology techniques (Immuological assays, electrophoresis, DNA hybridisation)
- Protein sequencing data available
- Data used to address questions regarding evolution
- Computers began to be used to compare sequences
- 1967 Fitch & Margolish perform the 1st study using sequence comparisons to assess phylogenetic relationships of Cytochrome C sequences in different organisms
1970s
- DNA sequencing
Matehematical algorithms formulated to understand sequences
1990s
- Contigs of sequence available
- Gene assignment based upon sequence homology
- Expansion of BLAST, alignment & phylogenetic methods
2000s
- Genomes
- Arrival of robust & fast sequencing methods
- Integration of complex mathematics into phylogeny (e.g. Bayesian)
~20 bullet points, but if you said Tufte to most scientists, they go "what?" Rather than even "who?" you say Dipity, they say doo dah.
So does the "kernel" need a rewrite for Phylogenetics? Seemingly they're gunning for a tree, partly from historical usage, and partly, because the models can't deal with other shapes yet (see also how some systems biology seemingly can't deal with feedback loops. Which are kind of important in Biological systems).
It made me think of Clay Shirky's write up on ontology here (audio here) and more specifically the File Systems and hierarchy section here. Probably the drawings - seeing the "just links, there is no filesystem set of pictures. There are plenty of articles about his talk, and lots of feedback on it e.g. here.
Seemingly, the system of phylogenetics was one of using a potentially shoddy model (knowingly), then retrofitting it - tweaking it to what the phylogenists (sp?) thought was right, then using giving it just a light dusting of scientific-ness.
A tree shape, only bifurcations, and problems with what lengths of things mean. There are several problem areas it seems. The problems of rooted vs unrooted trees. Molecular clocks? What happened to them? But decent is not exclusively vertical. Which causes problems - as the visualisation of the data, in the current way, can't show the complexity. Is this in part, a data visualisation problem? Some things, just can't be easily shown on a piece of paper in a journal.
Is phylogenetics having problems with it's pigeon holing? Doolittle's view that the history of life can't be properly represented as a tree seems to resonate for me. Why not visulise being statistically fuzzy with the lines of a tree at least? Are all changes equal in effect? Another problem.
Some other dates that could have gone in there, courtesy of the New Scientist article:
1990s
- DNA sequence of bacterial and archael genes becoming available, not just RNA. Some points, RNA saying A closer to B, but DNA saying A closer to C.
Unicellular archaea - an undiscovered major branch of the "tree of life" - previously thought of as bacteria were
So Horizontal Gene Transfer, is the Big furry Elephant sized problem in the phylogeneticist's room. When you've got people saying that Homo sapiens are an exception, there's a problem. When they're saying that in eukaryotes HGT is the rule rather than the exception, that's harder still. With bacteria and archaea and unicellular eukaryotes > 90% of life, with multicellular life just a small part of the word we live in, there's a problem. Also see endosymbiosis, and genome realignment, and presumably, several other mechanisms that'll effectively make the tree a thicket. You're back to being an archaeologist, looking for genetic fossils, to actually pin some dates and sequences down.
Then add a soupcon of the assumptions
- All mutations are independent
All mutations can reverse to a previous state
Mutation process are consistent through time
Mutations not influences by a previous mutation at that site
Lineages arise in a divergent tree-like evolution.
Fair bit on the methods at this point, which i'll add later. You've got to deal with 3rd base wobble (some changes have more or less meaning - ( i think she referenced information theory, but that's kind of hard to go over if you've not read up).
An unmentioned kicker - alignment is primary structure, not accounting for tertiary structure. So then you're playing around with mutation rates as a window-size average over the primary sequence it seems, with level of likelihood of change over a sequence.
So are the new methods the Emporer's new phylogentic garb?
Have there been any actually calculated fully tree spaces?
Is the list of alternative evolutionary processes, actually the other way round, and the current ones are the "alternative" though currently in fashion ones?
It seems there's potentially some confusion through looking at an organism at a gene by gene level, versus a genome level.
I wonder if this will come up on the exam.
"Darwin was wrong". The full article is here
Phylogenetics: what, how and when
So i'm listening and watching the presentation, and reading the article at the same time, and it felt at the time that more skepticism was needed. It's sometimes hard to gauge if the speaker means it when they say they'd like questions even during the talk. I'm all for asking questions, up to the point my coursemates get annoyed, and I get close to asking too many.
So go read the article linked above - The picture in the articke is close to that used in the 1st main slide, regarding "Phylogeny -a brief history" (which stated "the display of inferred relationships as a tree can be traced back to Charles Darwin) So that's inferred relationships. This is a model. There is no spoon.
The brief history covered the
1960s
- Origin of molecular biology techniques (Immuological assays, electrophoresis, DNA hybridisation)
- Protein sequencing data available
- Data used to address questions regarding evolution
- Computers began to be used to compare sequences
- 1967 Fitch & Margolish perform the 1st study using sequence comparisons to assess phylogenetic relationships of Cytochrome C sequences in different organisms
1970s
- DNA sequencing
Matehematical algorithms formulated to understand sequences
1990s
- Contigs of sequence available
- Gene assignment based upon sequence homology
- Expansion of BLAST, alignment & phylogenetic methods
2000s
- Genomes
- Arrival of robust & fast sequencing methods
- Integration of complex mathematics into phylogeny (e.g. Bayesian)
~20 bullet points, but if you said Tufte to most scientists, they go "what?" Rather than even "who?" you say Dipity, they say doo dah.
So does the "kernel" need a rewrite for Phylogenetics? Seemingly they're gunning for a tree, partly from historical usage, and partly, because the models can't deal with other shapes yet (see also how some systems biology seemingly can't deal with feedback loops. Which are kind of important in Biological systems).
It made me think of Clay Shirky's write up on ontology here (audio here) and more specifically the File Systems and hierarchy section here. Probably the drawings - seeing the "just links, there is no filesystem set of pictures. There are plenty of articles about his talk, and lots of feedback on it e.g. here.
Seemingly, the system of phylogenetics was one of using a potentially shoddy model (knowingly), then retrofitting it - tweaking it to what the phylogenists (sp?) thought was right, then using giving it just a light dusting of scientific-ness.
A tree shape, only bifurcations, and problems with what lengths of things mean. There are several problem areas it seems. The problems of rooted vs unrooted trees. Molecular clocks? What happened to them? But decent is not exclusively vertical. Which causes problems - as the visualisation of the data, in the current way, can't show the complexity. Is this in part, a data visualisation problem? Some things, just can't be easily shown on a piece of paper in a journal.
Is phylogenetics having problems with it's pigeon holing? Doolittle's view that the history of life can't be properly represented as a tree seems to resonate for me. Why not visulise being statistically fuzzy with the lines of a tree at least? Are all changes equal in effect? Another problem.
Some other dates that could have gone in there, courtesy of the New Scientist article:
1990s
- DNA sequence of bacterial and archael genes becoming available, not just RNA. Some points, RNA saying A closer to B, but DNA saying A closer to C.
Unicellular archaea - an undiscovered major branch of the "tree of life" - previously thought of as bacteria were
So Horizontal Gene Transfer, is the Big furry Elephant sized problem in the phylogeneticist's room. When you've got people saying that Homo sapiens are an exception, there's a problem. When they're saying that in eukaryotes HGT is the rule rather than the exception, that's harder still. With bacteria and archaea and unicellular eukaryotes > 90% of life, with multicellular life just a small part of the word we live in, there's a problem. Also see endosymbiosis, and genome realignment, and presumably, several other mechanisms that'll effectively make the tree a thicket. You're back to being an archaeologist, looking for genetic fossils, to actually pin some dates and sequences down.
Then add a soupcon of the assumptions
- All mutations are independent
All mutations can reverse to a previous state
Mutation process are consistent through time
Mutations not influences by a previous mutation at that site
Lineages arise in a divergent tree-like evolution.
Fair bit on the methods at this point, which i'll add later. You've got to deal with 3rd base wobble (some changes have more or less meaning - ( i think she referenced information theory, but that's kind of hard to go over if you've not read up).
An unmentioned kicker - alignment is primary structure, not accounting for tertiary structure. So then you're playing around with mutation rates as a window-size average over the primary sequence it seems, with level of likelihood of change over a sequence.
So are the new methods the Emporer's new phylogentic garb?
Have there been any actually calculated fully tree spaces?
Is the list of alternative evolutionary processes, actually the other way round, and the current ones are the "alternative" though currently in fashion ones?
It seems there's potentially some confusion through looking at an organism at a gene by gene level, versus a genome level.
I wonder if this will come up on the exam.
Wednesday, 28 January 2009
http://observationsofanerd.blogspot.com/2009/01/oestradiol-makes-women-hot-and-hard-to.html
"The estrogen hormone oestradiol is associated with just about every aspect of female beauty. As well as serving as a growth hormone for female reproductive organs, it's associated with having a symmetrical face, large breasts and a low waist-to-hip ratio. Now, the hormone is credited with one more association: it makes women serial monogamists."
""Are birth control pills changing modern women's mating strategies?"
Research into the Major Histocompatibility Complex has demonstrated that women tend to be attracted to men with substantially different genes in that region. This helps insure that offspring have a more efficient immune system. During pregnancy, the attraction is reversed. Women tend to prefer intimacy with people with like MHC, probably because their families will be supportive and protective of them during pregnancy and it is preparation for bonding with the offspring.
But when women are on the contraceptive pill, the hormonal effects mimic pregnancy. Thus, when on the pill, you're more likely to be attracted to men with a similar MHC. So if you meet your partner while you're on the pill, then go off the pill when you've decided you want a family, serious trouble can brew. Indeed, there is research supporting the notion that it is at exactly this point that a substantial number of marriages fall apart.
It also raises the issue of those offspring in relationships which started when the woman was on the pill. Is a substantial proportion of the subsequent generation going to have less effective immune systems?
"
http://journals.royalsociety.org/content/f542428772r96x64/fulltext.pdf
Sounds like this should be linked up with http://www.face-and-emotion.com/dataface/facs/description.jsp
Paul Ekman's work I think - on microslicing video, and predicting the strength of a relationship.
"The estrogen hormone oestradiol is associated with just about every aspect of female beauty. As well as serving as a growth hormone for female reproductive organs, it's associated with having a symmetrical face, large breasts and a low waist-to-hip ratio. Now, the hormone is credited with one more association: it makes women serial monogamists."
""Are birth control pills changing modern women's mating strategies?"
Research into the Major Histocompatibility Complex has demonstrated that women tend to be attracted to men with substantially different genes in that region. This helps insure that offspring have a more efficient immune system. During pregnancy, the attraction is reversed. Women tend to prefer intimacy with people with like MHC, probably because their families will be supportive and protective of them during pregnancy and it is preparation for bonding with the offspring.
But when women are on the contraceptive pill, the hormonal effects mimic pregnancy. Thus, when on the pill, you're more likely to be attracted to men with a similar MHC. So if you meet your partner while you're on the pill, then go off the pill when you've decided you want a family, serious trouble can brew. Indeed, there is research supporting the notion that it is at exactly this point that a substantial number of marriages fall apart.
It also raises the issue of those offspring in relationships which started when the woman was on the pill. Is a substantial proportion of the subsequent generation going to have less effective immune systems?
"
http://journals.royalsociety.org/content/f542428772r96x64/fulltext.pdf
Sounds like this should be linked up with http://www.face-and-emotion.com/dataface/facs/description.jsp
Paul Ekman's work I think - on microslicing video, and predicting the strength of a relationship.
Tuesday, 20 January 2009
The Unlikely Salsero - Seeing the Dance in Your Head article
Interesting to have a read of this - having had my first ballroom dance lesson recently (Social Foxtrot, Chachacha, some salsa to end). Whilst the best may yet be to come (Rumba, Argentian tango...) it was interesting to be throw into it - learning a start of a new pattern prior to even knowing the basic steps of the social Foxtrot.
I know that my partner commented that I kept on looking blank, and staring down at the floor -
A sign sometimes of heavy concentration and trying to visualise/go over the steps.
My thoughts also go back to getting Jules of LightStage fame hooked on salsa, so we could get some salsa done in one.
It would be a great visualisation tool.
http://uk.youtube.com/watch?v=sIwYpElarCk
Movement sensors, ultrasound emitters - all possible to be used: http://www.newscientist.com/article/dn12963
Can't find the information.
I know that my partner commented that I kept on looking blank, and staring down at the floor -
A sign sometimes of heavy concentration and trying to visualise/go over the steps.
My thoughts also go back to getting Jules of LightStage fame hooked on salsa, so we could get some salsa done in one.
It would be a great visualisation tool.
http://uk.youtube.com/watch?v=sIwYpElarCk
Movement sensors, ultrasound emitters - all possible to be used: http://www.newscientist.com/article/dn12963
Can't find the information.
Monday, 19 January 2009
Ultimate boys toys 2009
2008 list from Gizmodo: http://gizmodo.com/5106165/bestmodo-2008?skyline=true&s=x
Sony BDV-IT1000ES Bravia Theater System
Acoustic research FPS 10 Subwoofer
Nissan GT-R
Serious Materials EcoRock
Livescribe Pulse
Any camera that can do fast fps still shooting. Maybe RED will get there soon. (Not in the league of a Vision Research V12 or Phantom HD).
Sony BDV-IT1000ES Bravia Theater System
Acoustic research FPS 10 Subwoofer
Nissan GT-R
Serious Materials EcoRock
Livescribe Pulse
Any camera that can do fast fps still shooting. Maybe RED will get there soon. (Not in the league of a Vision Research V12 or Phantom HD).
Friday, 9 January 2009
Deep Brain stimulation
Thought experiment. If they got accurate Deep Brain Stimulation to work - would you use it? http://is.gd/f4eW- (Syndicate style?)
I always pondered - would there be a way to stimulate specific parts of the brain if you had orthogonal stimulators? One one side, another 90 degrees to it?
And if you could successfully do implants, why not? Or go through the nasal cavity, or the ears?
I remember the Royal Society had a small spot on one of theire open science days. There is a fair bit out there, of what happens when you stimulate neurons, and to behonest, it sounds like if you could do it accurately, it'd be bloody good fun, and highly addictive.
I always pondered - would there be a way to stimulate specific parts of the brain if you had orthogonal stimulators? One one side, another 90 degrees to it?
And if you could successfully do implants, why not? Or go through the nasal cavity, or the ears?
I remember the Royal Society had a small spot on one of theire open science days. There is a fair bit out there, of what happens when you stimulate neurons, and to behonest, it sounds like if you could do it accurately, it'd be bloody good fun, and highly addictive.
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