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Basil last won the day on June 23

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About Basil

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  • School
    Iowa State
  • Level of Education
    Currently Doctoral/Medical

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  1. Data Science Poll 8/13/17 If you utilize cloud computing, which service provider do you currently use?
  2. How Important is GRE for Ph.D Programs?

    Stephanie has the right idea. GRE scores are an important part of somebody's application. However, other factors are crucial as well (like she mentioned.) Every program is also different, and most programs will state on their homepage the average GRE percentile for those admitted into the program. This can help you gauge your competitiveness for a program, and also offer you a target score if you have not taken your test yet.
  3. Convering hg19 to hg38

    It uses chromosomal regions in the BED file format. For this type of file, there are three required pieces of information needed: Chromosome Number Chromosome Start Chromosome End So for example, if you're dealing with a gene on chromosome 16 that spans the regions 53,701,692 to 54,158,512, it would look like the following in a BED format file: chr16 53701692 54158512 BED files are usually designated with the .bed file format, but in the case of liftover, you can simply open your text editor, make sure your genomic coordinates are in the format I described, and paste it in on the website.
  4. Here's another Data Science Poll! Let us know what programming language you currently utilize the most! If the language you use is not one of the options, please post it below!
  5. I wIsh you the best of luck on your application! Let us know if you need any advice anything in regards to your application!
  6. Extracting Reads from BAM and SAM Files

    If you're trying to extract reads from a BAM/SAM file that is small enough, you can simply use a Linux command. A combination of GREP and CAT will do the trick. Something like: Cat file.sam | grep myreads.txt If the file is a little too big for that, you can use PicardTools and the feature FilterSamReads. This will allow you to extract from the SAM file specific reads of interest. Here's an example usage for PicardTools. java -jar picard.jar FilterSamReads \ I=input.bam \ O=output.bam \ READ_LIST_FILE=read_names.txt FILTER=filter_value BTW, if you've never used PicardTools before, you simply download the file, and move it to the directory you are working with (or just call it from whatever directory you desire.) There's no installation needed.
  7. Do Ph.D Programs accept MCAT scores

    Every program is different. For example, Ohio State's Biomedical Informatics Ph.D. Program allows for MCAT scores to replace GRE scores in certain situations, whereas Oregon Health and Science University's Biomedical Informatics Program does not. There's still a lot of time before many of these programs open up their application, so I would recommend going ahead and taking the GRE. Although the MCAT and GRE are extremely different, you at least have the experience of preparing and sitting through grueling standardised tests.
  8. More Informatics blog posts

    We would love to expand our blog section with more topics and wouldn't mind recruiting more writers! If you'd like, you can either create your own blog by clicking this link and then selecting the "create blog" option. Or, send me a private message, and I can give you access to any of the existing blogs, where you can make contributions.
  9. A New open-source software has been developed by researchers from Cold Spring Harbor Laboratory and John Hopkins University, to address the need for more accurate measurement of protein translation. Named Scikit-ribo, the tool enables accurate aminoacyl site prediction and estimates of translational efficiency from either Ribo-seq or RNASeq data. The software can be downloaded from the Scikit-bibo Github page, https://github.com/hanfang/scikit-ribo. Additionally, Scikit-ribo was published in the bioRxiv preprint server at the following link: http://www.biorxiv.org/content/early/2017/06/27/156588
  10. PathwayMapper Although there are many visualization tools available, that allow researchers to explore and analyze their cancer datasets, not many of them provide simplified diagrams. To answer the need for simplification, researchers from Bilkent University, Cornell University, and Oregon Health and Science University have a developed a new online tool. Named PathwayMapper, the web editor allows researchers to create more clear pathways and diagrams, similar to those found in The Cancer Genome Atlas. The online tool can be accessed via the PathwayMapper website (www.pathwaymapper.org) or can be downloaded from the PathwayMapper's Github Page. Our Interaction with PathwayMapper Our brief interaction with the online web version of PathwayMapper showed us just how easy it was to develop sophisticated pathways while keeping things easy to follow and understand. Users can quickly select different node palettes such as the particular gene, complex, family, etc. Another category allows you to create the various interactions that are occurring between the complexes. Additionally, the software allows you to create customizations to the layout, that gives you the most control over the entire design of the pathway.
  11. First off, thanks for becoming a YDSOA member. I hope to see you around the site! Bioinformatics and Medical Informatics have a lot of similarities, utilize a lot of the same principles, etc. However, Medical Informatics (or Health/Biomedical Informatics) differs from Bioinformatics in that it is heavily tied into the work of clinicians. Bioinformatics can have a clinical component to it (i.e., Translational Bioinformatics), but it has a much broader reach. There are scientists involved in plant studies, the microbiome, and other species besides humans, that rely on Bioinformatics. So if you know for a fact that you only want to work with clinical data, Health/Medical Informatics is more than likely the best route. If you are open to a wider range of applications, Bioinformatics would be useful to look into. The ideal route would be to find a list of schools that you are interested in applying to and look to see whether they have a Bioinformatics program, a Health Informatics program, or both. Then focus on the researchers that you might be working under, through each of the programs. I would then apply to the schools, and the related program, based upon this overlap.
  12. Vincent Granville over at DataScienceCentral has an excellent article about the six categories of Data Scientists. That begs the question, for all the Data Scientists who are members of YDSOA, which one of these areas would you like to get more involved in, either in your job or your research?
  13. Choosing a Rotation Lab

    Great question. First of all, finding labs to rotate in and choosing your home lab are entirely unique situations to have to deal with. Obviously, the latter is a much tougher and more urgent situation to deal with. While filling those rotations might be a more superficial process, there are some things you'll want to consider. Research Interests: You'll only want to rotate in labs that fit your research. Face-to-Face Interview: Were you given a chance to meet potential advisors during graduate interviews? If not, find some advisors that align with your interests, and schedule a face-to-face meeting. This is extremely important and allows you to get a feel for what the adviser is all about, and what your role in the lab would be. Word of Mouth: It's always an excellent idea to talk to other students who have either rotated in the lab or are currently members of the lab. Be sure to ask around and talk to multiple students, as you'll always run into 1-2 students who may have had bad experiences in the lab, but these isolated experiences aren't accurate representations of how the lab would be. After filling the spots, it's now time to shift your focus on the rotations themselves. This is where you can gauge your experience across the weeks or months during the rotation. Some questions you need to assess: What kind of environment is the actual lab like? Can you imagine yourself spending four, five or even six years there? How does your research fit with your interests? Sometimes during the face-to-face interview, you get the sense that the lab might be up your alley, regarding research, but once you do your rotation, you might find out that they deviate away from your passions. How much personal and educational growth do you believe you can achieve by joining this lab? How do you feel about your advisor? Gauging somebody from 1-2 interviews is hard. Seeing how your interact with your adviser across weeks and months is when you can truly see how well you work with them? What is the school/life balance in the lab? There's one last important thing I want to mention: Lab rotations are a two-way street. Not only are you seeing if a particular lab is a good fit for you, but your potential adviser is also looking to see if you are a good fit for them. Make sure to keep this in mind! Hope that helped!
  14. Data Science has shaped the career paths for thousands of individuals around the world. The #WhyDataScience initiative is a way for Data Scientists let others know how the field has shaped their career paths and why they chose the field. The goal of the project is to compile a huge database that inspires the next generation of Data Scientists. More information on the project will be released in the upcoming weeks!
  15. This is some awesome advice! Thanks for sharing it, Stephanie!