Forum:Bioinformatics assistance for severely visually impaired bioinformatics graduate student needed

Question

[Thomas.F.Hahn3]

I am a severely visually impaired bioinformatics graduate student. I need help in getting an overview of current techniques, methods and approaches for using genomic and other publically available data to make predictions and conclusions. Since I am legally blind I cannot achieve this objective by reading but rather I need an assistant to compensate for my visual disability. Based on this overview we need to write a literature review and then write a PhD dissertation proposal, which needs to be presented in the middle of August of 2016 and that can be completed within one year because I only have funding until May 15th, 2017. Due to lack of funding, only publically available data are available to be used for analyses in my bioinformatics PhD dissertation research.

Possible websites to look for suitable datasets for analyses are: 1) https://www.ebi.ac.uk/arrayexpress/

2) http://www.ncbi.nlm.nih.gov/sra I am thankful for any additional suggestions.

Possible aims of my bioinformatics dissertations are:

1. Predicting genes or combinations of genes that when over-or under-expressed can extend lifespan preferably in yeast but also other species are possible. We are interested in identifying changes in gene expression patterns that can be associated with an increased lifespan.

2. Better understand how and why caloric restriction can extend lifespan in yeast.

3. Identifying the factors that are responsible for a queen bee to live for up to 4 years whereas their genetically identical worker bee counterparts only live for a few weeks.

4. I am generally interested in making my bioinformatics dissertation a contribution to better understand and delay aging. Any approach to accomplish this is very welcome.

We can also define other aims if they are suitable for a bioinformatics PhD dissertation. So if you are already good in any techniques, methods or approaches and would like to train me in how to use them for my dissertation, I am very interested in your suggestions. Meta-analyses are also possible if we can find ways to compare data from different studies. I am very open and thankful for any kind of suggestions, ideas and recommendations since I am overwhelmed with the visually too demanding selection process for finding and implementing the best methods, techniques and approaches given the conditions described above because I am legally blind.

If you are interested in assisting me in any way to make progress with my bioinformatics PhD dissertation despite me being legally blind, please email me at [e-mail] or send me a Skype invite to my Skype ID, which is tfh002.

I am very much looking forward hearing from you.

With very warm regards

Thomas Hahn

[Istvan Albert]

Hello Thomas,

I think your project goals are too ambitious - this is a universal problem in bioinformatics in general. Your three subject areas are only superficially (if at all) related - and each is complex on its own. In addition from you post it is not clear at all what the request for help implies. None of us here have a good sense of what the responsibilities of a bioinformatics assistant to a legally blind person are. They sound very difficult actually.

My personal suggestion is to step back a level and write your dissertation not on aging itself but what is it like to be a visually impaired bioinformatician. How does one even go about it? What should we change in this field of science to make it more accessible to the visually impaired?

Your findings would make a bigger impact for you and everyone else that is affected. It is fine to frame this inquiry in the context of one of your research goals as well. Still in my opinion the focus should be on improving bioinformatics for the visually impaired rather than just making your own scientific discovery. And I am convinced that this will make bioinformatics more accessible and easier for everyone else as well.

For example we would be interested in providing alternative page rendering in Biostar that supports text-to-speech engines. And with that we could make Biostars a test platform for distributing Q&A type information for the visually impaired.

[Giovanni M Dall'Olio]

Ronald Fisher was also almost blind. His vision was so poor that he was not able to write mathematical solutions, yet he became able to solve complex mathematical problems by imagining them in his mind. His contributions to population genetics were so important that he is considered one of the three fathers of the field.

Answer 1

[LLTommy]

Hi there, I think it is great that you want to overcome your disability. Good luck with that and I hope you find somebody that can help you out! However, I have to say, I am confused by what you tell us. I never came across an institute where it was possible to get a phd in a year, or actually 10 months! I know many people that spent more time on their Master Thesis! I always was told that a phd takes at least 3 years - most often it is more than that! And quite frankly I also think that it should be that way, I don't think anybody should get a phd for a project of 10 months. So, I think this part of your plan sounds strange! And I think you should talk with your supervisor about it, this does not at all sound like it's enought time for a phd project!

Answer 2

[John]

Unfortunately your goal of doing a PhD in less than a year is impossible. Even with an assistant it would take several years of working long days and weekends to get a PhD. Any PhD.

But that isn't the big problem. The big problem is that bioinformatic software is particularly poorly suited for people with visual impairments. Of course being legally blind may mean you have some ability to read printed text given magnification, high contrast screens, etcetera, so how difficult you will find using bioinformatic software will depend on the specifics of your condition and the tools that are available to you. However, if you are unable to read printed text then pursuing a career in bioinformatics would be extraordinarily difficult, because the tools are often designed with little to no consideration for the user experience, which is something that infuriates everyone. Of course there are exceptions, many of the users on this forum write excellent software, but the general lack of time, effort and money put into making bioinformatic software accessible to people is a well known problem, and likely to change in the next 5 years. However, and i'm just trying to be realistic here, you want to be done with the PhD by the time that accessible software exists, not just starting.

Outside of bioinformatics but within biostatistics, your options look a lot more promising. There have been numerous attempts to make R better for visually impaired users, and if you haven't already read it I highly recommend this article from 2013 https://journal.r-project.org/archive/2013-1/godfrey.pdf

If you stay within mainstream statistics and data analysis, and use popular tools like R, Matlab, Mathematica, and others, but working on new data or thinking of new analyses, then I think your chances of success and also happiness will increase dramatically.

On the flip side, as Istvan mentioned in his comment, there is clearly a lot you could teach the developers of Bioinformatic tools on how to make accessible software. The question is, would that count as original research required for a PhD. I don't know. On the other hand, if you only have a year for a project, I can imagine that would be a very productive year.

Answer 3

[WouterDeCoster]

Dear Thomas,

That's not immediately the kind of questions we are used to here! I think most of us, including myself, have no idea about what extra hurdles a PhD for you means. Therefore, it might be useful if you can be a bit more specific with regard to what help or solutions you expect (from us). Specific questions result in specific answers (both here and in your research).

With regard to your topic(s) I think there is a wealth of public data out there, especially for expression studies, e.g. GEO (free) and genevestigator (not entirely free). Often, data is used to answer a specific question and then (luckily) deposited in a repository. I think the public data out there has a lot more answers than what we already queried it for. But I think it might be interesting if you or someone else at your institution could test some hypotheses and validate some results, e.g. in C.elegans, a model often used for caloric restriction and life span studies.

However, I agree with the comment made by LLTommy. During a PhD project (everyone, in any PhD project) you'll experience unforeseen difficulties and just learning how to work with tools will take a lot of time until you orient yourself to what you aim to achieve. As such, you might need more time than what you describe. Perhaps there are people at your institution who can inform you about additional funding options. Nevertheless, if this is your only option I wish you the most of luck and success with your projects.

Answer 4

[natasha.sernova]

Dear Thomas,

I understand your problem very well.

First of all you need tools to listen to the articles in English.

I think you've had links like that, but some more ones are better than nothing.

http://www.naturalreaders.com/index.html

http://www.investintech.com/resources/blog/archives/5301-convert-text-speech.html

Another thing you will definitely need, a tool to reach papers having only their doi or something similar:

http://sci-hub.cc/

I hope it will help you.

Unfortunately I do not study aging, yeasts or insects.

[MAPK]

I would add voicedream reader on the list. The best app for this purpose.