Job:Research advice needed

Question

[tfhahn]

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 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.

I need help to quickly get a publication of any sort to be allowed to continue in the program. If you have any idea please contact me quickly.

[Giovanni M Dall'Olio]

Where are you based? Is there any local community of bioinformaticians that could help you?

[tfhahn]

I am based in Little Rock, Arkansas, USA. For some strange reason I cannot get local support. Its a long story and hard to explain. All everyone wants me to do is to graduate asap because funding will be over in June.

Answer 1

[Michele Busby]

Please forgive me but I am going to jump in with some wildly unsolicited advice.

This sounds like your are in a really bad situation which has nothing to do with your visual impairment.

In the US, we generally have an adviser who guides us to the topic we will study. In the UK, there is usually a project set up before the student joins. One of the things you learn in a PhD is how to select topics that are worthy of study. It is not usually something you would be expected to come in knowing. Then it takes several years (usually at least 3) to complete. So before you embark on your dissertation you would have several years of research under your belt, usually starting by helping someone else and then taking more ownership of the project as you go along.

It seems like you are either not getting appropriate advice from an adviser and you are not in a lab with adequate funding.

That said, I had an idea for a project that I didn't have time to do before I left industry. It should make a good small comp bio paper and can use publicly available data. It is on ChIP Seq, not aging though, and it is methods development. I will send to you if you are interested. You can get to me at busbym at bc edu

[tfhahn]

Hi. That would be good. I have never analyzed chip seq datasets before. Would you be able to teach me?

[Michele Busby]

I can probably only get your started.

Are you able to look at things like IGV?

[tfhahn]

What is IGV? I have a screen magnifier. It can magnify most of the things. Could we please connect on Skype? My Skype ID is tfh002. You can also call me at my cell phone at 318 243 3940

[GenoMax]

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

[Michele Busby]

Hi, try sending me an email and I'll set something up.

Thanks, Michele

[tfhahn]

Thank you Michele. I just replied to your twitter account. I have completed my work for today and I am free to start working on it any time now. I still plan to work at least for a few hours in my office at the university because only here I have fast internet and a 50 inch huge screen connected to my laptop. You are very welcome to email me anything at any time to [e-mail].

Once you have emailed me could you also please call me at my cell phone so you can explain me by voice how to proceed since I can follow spoken instructions much better than written instructions because although I can still read with high Zoomtext magnification this process is slow, exhausting and error prone because I need so high magnification that I'll lose orientation on the screen quickly.

My cell phone number is 318 243 3940. If I don't pick up, then its because cell phone reception is generally poor here on the fifth floor in our new bioinformatics buildings, where my GA office is located. Then you can try my office landline at 501 682 1440. We could also connect on Skype because that would allow me to share screens with you so you can see whether I am using what you'll send me correctly. What is your Skype ID? My Skype ID is tfh002. Could you please send me a Skype invite?

We could also connect remotely with Team Viewer or Any Desk. Those are free computer remote control programs you can download and install for free. This has the advantage that I can follow every stop you take on my computer with as much Zoomtext magnification I'd like automatically without needing to track the mouse or cursor. Zoomtext is the software I need to read and work with computers because it can magnify and read word, html and pdf files. Here is the link to this software so you can better understand why it takes me much longer to find things on my screen or hard drive unless I know exactly where I need to scroll with my high powered magnified window, which unfortunately only covers a very small area, to find what I am looking for. See https://www.aisquared.com/products/zoomtext/ for details

That is why one on one remote computer training session are so helpful to me. They allow me to work even with graphically very demanding interfaces as long as somebody has taken the time to train me until I know by heart in which direction I need to scroll to find a particular function or button.

Using this approach I could slowly learn R, MATLAB and even the graphically completely overloaded and very confusing web applications of the Broad Institute, which were so unforgiving to any kind of formatting errors in the data input files without telling what needs to be changed so that they'll read in the files correctly, that I stopped using them.

My approach of using remote access programs, such as TeamViewer or AnyDesk, in combination with Zoomtext and Skype, has impressed the organizers of the 18th International ACM SIGACCESS Conference on Computers and Accessibility in Reno last October (see https://assets16.sigaccess.org/) so much that they published my conference proposal in the ACM Digital Library. You can find it under the following citation if you have access to the ACM publications:

1) Thomas Hahn, Hidayat Ur Rahman, Richard Segall, Christoph Heim, Raphaela Brunson, Ankush Sharma, Maryam Aslam, Ana Lara-Rodriguez, Md. Sahidul Islam, Neha Gupta, Charles S. Embry, Patrick Grossmann, Shahrukh Babar, Gregory A. Skibinski, Fusheng Tang. 2016. Remote Access Programs to Better Integrate Individuals with Disabilities. In Proceedings of the 18th International ACM SIGACCESS Conference on Computers & Accessibility (ASSETS '16). ACM, New York, NY, USA, 245-250. DOI=http://dx.doi.org/10.1145/2982142.2982182, ISBN: 978-1-4503-4124-0

[tfhahn]

I think only once you see my pictures, which show the different perspectives, what I am trying to explain will suddenly make sense for people, who have never seen a screen magnifier at work. So if you have no access to the electronic ACM Library, but still would like to see it how it works, please let me know and I'll email you a copy of my manuscript, which I submitted to this conference.

When I presented my approach at this accessibility computer conference last year, which had saved me so many times from having to drop out of graduate school as long as I could find a dedicated competent sighted trainer, I could convincingly prove that my remote peer-training approach can really push back the inherently initially unavoidable and insurmountable-seeming limitations, which everyone, who depends on a very small effectively remaining visual field, appears to be inevitably confronted with, because I could convincingly prove, that through proper and repetitive training the imaginary visual field, i.e. the imaginary mental visual map our mind can create from its memories of the visual inputs from past training experiences about the relative location of all relevant objects to one another, is a very highly effective - but unfortunately still much under-utilized - way of imaginary re-expanding the narrow boundaries of the realistically existing and objectively measurable very small effectively remaining visual field by more than 100 times.

Its kind of amazing that navigating through such kind of imaginary visual memory, which - although initially requiring visual input from the very small effectively remaining visual field for initially creating the necessary visual memories and experiences for gradually developing a functional imaginary model of the remembered relative spacial relationships between the objects encountered when scrolling the screen with the effectively remaining very small but realistically existing visual field - no longer requires functional eyesight to complete the same tasks, for which normally the realistically existing and effectively remaining very small visual field would be otherwise needed, as long as reality is not changing after the imaginary model was created from its memories.

That is why I hate companies, journals and other entities for changing the layout of their websites and interfaces just to look trendy and modern because this instantly inevitably renders all my imaginary visual memories, on which I am heavily depending to re-expand the narrow boundaries of my effectively remaining very small visual field, which took so much efforts, time and many repetitions until a functionally usable imaginary model of the relative spacial relationships between the objects encountered with the very small effectively remaining visual field could gradually develop, as utterly useless over night because suddenly it would be better if these now false imaginary models would have never been created in the first place.

I just wanted to tell that theoretically, I can still learn almost every - no matter how complex - task on computer as long as I can find people, who patiently assist me in creating a functional model of the things I saw in reality in my imaginary visual memory by patiently practicing with me until I can perform all its functions on my own.

Oh, and in case you discover that there is no more space for leaving me voicemails, which has been a common problem lately, you can call my Google Voice number, which is [phone]. This is my only number, which always has plenty of space even for the longest voicemails.

Answer 2

[Petr Ponomarenko]

It is so great to see people so much dedicated to bioinformatics. I would love to help you. However, it is a lot of work to be completed in a very short time if May 15th, 2017 is the deadline. Please accept my invitation in skype. Thank you, Petr