So, I've been playing around trying to define my PhD project. My interests are in visualisation and integration of biological information. I've done some other small projects in this field, but I haven't been able to find a project that fully interests me and that I can use what I have been working on for the last couple of years. Until now...
In the last meeting with my supervisor we were talking about different projects that our lab is involved in, and a common problem on those was the difficulty of moving the information from different domains, which means, for example, that the data obtained in a microarray experiment is hard to put it in context with genomic and proteomic information at the same time, i mean that is possible but it always requires extra work.
Other big issue is that thanks to high throughput technology the amount of generated data is massive!! I'm talking of files in the order of tens of gigabytes. And thats the kind of data we have to deal with. So whats my idea? Simply a tool fully configurable to visualize biological information from multiple domains. Pretty cool eh?
Well if you are in the bioinformatics field that sounds like one of the holy grails in our field. So yeah, thats what I'm gonna do. Oh well, thats pretty ambitious, but there is a lot of work done on it and I think big part of this mission is putting pieces together, for instance a good friend is working on a library of JavaScript components for biology, so I plan to use a lot of those. Another friend developed a protein annotation viewer based on DAS called Dasty, and it has a really nice architecture based in plugins, I know this because I helped in the design :-). Other friends have worked visualising genomic information, specially focus in personal genomics(myKaryoView). I also did some collaboration there.
And that's why I think I can came up with something useful and cool, but knowing myself I have to keep the motivation high, and thats where this blog became important. I will try to post at least once every 2 weeks reporting the progress that I have done, if any, and in that way force myself to do something to be able to write something. We'll see how it goes.
For now I started writing the requirements and drawing some sketches of my ideal interface, I will show those in my next post. So, for now wish me luck and please give me ideas about the project.
Just to finish, I want to say that although the genomic information maybe the central part of my project the motto of this project will be BIOsual: Not just another genome viewer.
In the last meeting with my supervisor we were talking about different projects that our lab is involved in, and a common problem on those was the difficulty of moving the information from different domains, which means, for example, that the data obtained in a microarray experiment is hard to put it in context with genomic and proteomic information at the same time, i mean that is possible but it always requires extra work.
Other big issue is that thanks to high throughput technology the amount of generated data is massive!! I'm talking of files in the order of tens of gigabytes. And thats the kind of data we have to deal with. So whats my idea? Simply a tool fully configurable to visualize biological information from multiple domains. Pretty cool eh?
Well if you are in the bioinformatics field that sounds like one of the holy grails in our field. So yeah, thats what I'm gonna do. Oh well, thats pretty ambitious, but there is a lot of work done on it and I think big part of this mission is putting pieces together, for instance a good friend is working on a library of JavaScript components for biology, so I plan to use a lot of those. Another friend developed a protein annotation viewer based on DAS called Dasty, and it has a really nice architecture based in plugins, I know this because I helped in the design :-). Other friends have worked visualising genomic information, specially focus in personal genomics(myKaryoView). I also did some collaboration there.
And that's why I think I can came up with something useful and cool, but knowing myself I have to keep the motivation high, and thats where this blog became important. I will try to post at least once every 2 weeks reporting the progress that I have done, if any, and in that way force myself to do something to be able to write something. We'll see how it goes.
For now I started writing the requirements and drawing some sketches of my ideal interface, I will show those in my next post. So, for now wish me luck and please give me ideas about the project.
Just to finish, I want to say that although the genomic information maybe the central part of my project the motto of this project will be BIOsual: Not just another genome viewer.
Viejo Gustavo, interesante parcero, pero solo un comentario, si me lo permitis: no escribas todo de una, metele espacios, saltos de linea. pequeñas ayudas que facilitan la lectura a los que usamos gafas jejeje
ReplyDeleteTe cuidas parce, un saludo.
Att. Julian B
Gracias Julian! Bakano saber de vos y si acabo de hacerle una pequeña edición al documento y tratare de seguir tu consejo pa la próxima.
ReplyDelete