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.
Wednesday, 20 May 2009
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
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