This is the assignments page for BIOL.635.01 - Bioinformatics Seminar (BIOL63501.2161), an online course at
Rochester Institute of Technology, for Fall 2016. If you are a student in the course, please return to this
page every week to look for updates. Updates will be posted no later than Monday evenings to be available by
the following Tuesdays.
Assignment 1: Assigned, Tuesday 23 August 2016; due Tuesday 30 August 2016.
2. Sign up for a Google account (https://accounts.google.com/signup), and,
using your gmail account, send your gmail address to the instructor at his gmail address ()
3. Using your Google account, start a blog for your work in this course (see https://www.blogger.com/). Blogs use a global name space.
To avoid conflicts, begin the name for your blog with your Google ID followed immediately by
the name BIOL635F16, e.g. http://yayahjbBIOl635F16.blogspot.com/
4. Using your Google account, start a personal course web page on which to post papers and presentations for this course.
If you already have a public web page, you may use a subpage of that web page instead, provided the papers and presentations
will be public. You must make your blog posts and all your papers and presentations public. Be very careful about what you post,
both in terms of respecting the intellectual property of others and in terms of being very sure that what you post is material
that you are willing to make public. This may seem daunting, but you must get used to it if you are every to be successful at
scientific publication.
5. Prepare your first paper and presentation. This paper and presentation must be related in some way with some recent
paper published in BMC Bioinformatics (http://www.biomedcentral.com/bmcbioinformatics). Do not worry about conflicts or overlap with other students,
but each person must do their own work.
The presentation must be exactly 15 slides, beginning with a title slide
and ending with a references slide, leaving you 13 slides in which to tell a coherent scientific story. Don't jam too
much material onto each slide. These constraints may seem artificial and daunting, but learning to cope with them is
important.
6. No later than 8 pm on Thursday, 25 August 2016, prepare a list of any problems you are having with this assignment for
discussion at the course group e-meeting, and email that list to the instructor. Try not to miss this first e-meeting, because
you will have two more assignments to work on before the next one.
7. Describe everything you have done for this course up to this point in your course blog. Be sure to include links to
your paper and presentation
Assignment 2: Assigned, Tuesday 30 August 2016; due Tuesday 6 September 2016.
1. Be sure to complete assignment 1, above, especially getting your blog started.
2. Pick your personal topic area on which you will focus for the rest of the semester. Recall from the syllabus that
"At the time Michael Osier proposed this course in 2011, the list of topics was: Genome sequence analysis, Signals in sequences, Gene
expression analysis, Ontologies, Data and text mining, Structural bioinformatics, Phylogenetics, Systems biology. These remain appropriate
topics. In addition, there is a great deal of current work on the informatics issues in Rational drug design, the 'Big-data' implications
of bioinformatics and new data acquisition techniques, the Eigenproblems of data mining and hierarchical clustering." If you do not
have a topic you prefer, then you should focus either on big-data in bioinformatics or the eigenproblems of data mining in bioinformatics.
3. Working within your chosen focus topic, go to scholar.google.com and find the most recent paper in your focus topic that is
accessible to you immediately, read that paper and ...
4. Prepare your second paper and presentation. This paper and presentation must be prepared with the paper conforming to the BMC
Bioinformatics Instructions to Authors (http://www.biomedcentral.com/bmcbioinformatics/authors/instructions), especially in terms
of the style of references.
5. You are reminded that you are not simply to regurgitate what you read in your selected paper. You are to do substantial reading
and research so that you actually understand what you are discussing. You must present the state of the field in which the work was
being done, and how this paper fits in and what it contributes. You must be _very_ careful not to cut and paste or simply paraphrase
the text of the paper, but to engage your brain and put in the time and effort to do a proper critical review of the paper you choose.
If you are unable to do a decent job on the first paper you choose, choose a different paper.
6. The presentation must be exactly 15 slides, beginning with a title slide
and ending with a references slide, leaving you 13 slides in which to tell a coherent scientific story. Don't jam too
much material onto each slide. These constraints may seem artificial and daunting, but learning to cope with them is
important.
7. The paper must be a properly structured paper with real content, reflecting real research. It will take you several hours
of intensive work to do this even if nothing goes wrong. The paper should reflect that level of effort.
8. You will receive indivdual comments on what you did or did not do for assignment 1, but from what I have seen so far, some
of you will have to redo your first assignment. Feel free to get a head-start on that, but do the second assignment first.
Don't panic if you feel that you did not show your best work in the first assignment. The point of this course is to learn to do
this well. If you
already were expert at it, you would not need to be taking the course.
9. Describe everything you have done for this course up to this point in your course blog. Be sure to include links to
your papers and presentations.
Assignment 3: Assigned, Tuesday 6 September 2016; due Tuesday 13 September 2016.
Be sure to complete assignments 1 and 2, above, especially getting your blog started and getting ready to present. At the
group emeeting this week, every student will be required to discuss the state of their work on the first two assignments and to
present one of those two (preferably the second one). The
regular group e-meeting will be on Tuesday, 6 September at 8 pm.
Have a coherent timed two-minute report on what you have done for this course ready to present. Have
a single slide ready. Every student will present their slide, as many students as possible will also present
one of the two presentations they have worked on. The choice of which students present will be made during the e-meeting on the
basis of the two-minute reports.
I will be providing written feedback on the work you have submitted thus after these presentations. I have held off because
the
return thus far has been sparse. I cannot give you feedback on what you have not submitted, so please submit what you can on the
first two assignments no later than Tuesday evening. It would be unfair to the students who have kept up to delay any longer
than
that.
Working within your chosen focus topic, go to scholar.google.com and find a different recent paper in your focus topic that
is accessible to you immediately, read that paper and ...
Prepare your third paper and presentation. This paper and presentation must be prepared with the paper conforming to the
Journal of Structural and Functional Genomics Instructions to Authors (
http://www.springer.com/life+sciences/biochemistry+%26+biophysics/journal/10969), especially in terms of the style of
references.
You are reminded that you are not simply to regurgitate what you read in your selected paper. You are to do substantial
reading and research so that you actually understand what you are discussing. You must present the state of the field in which the
work was being done, and how this paper fits in and what it contributes. You must be _very_ careful not to cut and paste or simply
paraphrase the text of the paper, but to engage your brain and put in the time and effort to do a proper critical review of the
paper you choose. If you are unable to do a decent job on the first paper you choose, choose a different paper.
The presentation must be exactly 15 slides, beginning with a title slide and ending with a references slide, leaving you 13
slides in which to tell a coherent scientific story. Don't jam too much material onto each slide. These constraints may seem
artificial and daunting, but learning to cope with them is important.
The paper must be a properly structured paper with real content, reflecting real research. It will take you several hours
of intensive work to do this even if nothing goes wrong. The paper should reflect that level of effort.
Describe everything you have done for this course up to this point in your course blog. Be sure to include links to your
papers and presentations. Email the url of your blog to the instructor.
Assignment 4: Assigned, Tuesday 13 September 2016; due Tuesday 20 September 2016.
Be sure to complete assignments 1, 2, and 3 above, especially getting your blog started and getting ready to present. At
the group emeetings this week, every student will be required to discuss the state of their work on the first three assignments.
The regular group e-meeting will be on Tuesday, 13 September at 8 pm. Have a coherent timed two-minute report on what you
have done for this course ready to present.
Have a single slide ready. Every student will present their slide and as many students as possible will also
present one of the three presentations they have worked on. The choice of which students present will be made during the e-meeting
on the basis of the two-minute reports.
By Tuesday 20 September, you should have done research based on 4 papers. It is time to start to pull the research effort
together and to make a whole that is much more than the sum of its parts. You are to select a reference manager (see
https://en.wikipedia.org/wiki/Comparison_of_reference_management_software) and to start gathering all your research citations in
that manager. Your are to record your selection in your blog and provide a link to your growing bibliography on your web site. At
the end of the semester you will be required to use this resource to produce an annotated bibliography on your research topic. I
cannot tell you which reference manager to choose. The right one for you may be completely different from what is right for me or
for another student. Factors to consider are what type of computer you use, what word processing software you use and what
journals you are likely to want to publish in. For my own work, I use a mac with TexShop, and my reference manager is combination
of bibtex with JabRef. I collaborate with others who use Word on macs and PCs and who prefer Zotero. You must do your own research
on what reference manager to use and pick one this week. If you make a mistake and want to change later, you may do so, but you
need some version of this tool now.
Working within your chosen focus topic, go to scholar.google.com and find a different recent paper in your focus topic that
is accessible to you immediately, read that paper and ...
Prepare your 4th paper and presentation. This paper and presentation must be prepared with the paper conforming to Nature
Communications Guide to Authors (
http://www.nature.com/ncomms/authors/index.html), especially in terms of the style of references.
You are reminded that you are not simply to regurgitate what you read in your selected paper. You are to do substantial
reading and research so that you actually understand what you are discussing. You must present the state of the field in which the
work was being done, and how this paper fits in and what it contributes. You must be _very_ careful not to cut and paste or simply
paraphrase the text of the paper, but to engage your brain and put in the time and effort to do a proper critical review of the
paper you choose. If you are unable to do a decent job on the first paper you choose, choose a different paper.
The presentation must be exactly 15 slides, beginning with a title slide and ending with a references slide, leaving you 13
slides in which to tell a coherent scientific story. Don't jam too much material onto each slide. These constraints may seem
artificial and daunting, but learning to cope with them is important.
The paper must be a properly structured paper with real content, reflecting real research. It will take you 9-12 hours of
intensive work to do this even if nothing goes wrong. The paper should reflect that level of effort.
Describe everything you have done for this course up to this point in your course blog. Be sure to include links to your
papers and presentations. Email the url of your blog to the instructor.
Assignments 5 and 6: Assigned, Tuesday 20 September 2016; due Tuesday 27 September 2016 and Tuesday 4 October 2016.
Note: This is a double assignment to allow sufficient time for an inter-library loan. In this assignment, one of the papers you
will review may not be immediately accessible and you may need time for an inter-library loan.
Be sure to complete assignments 1 - 4 above, especially getting your blog started and getting ready to present. Have a coherent timed
two-minute report on what you have done for this course ready to present. Have a single slide ready. Every student will present their slide,
and at each group e-meeting, as many students as possible will also present one of the presentations they have worked on. The choice
of which students present will be made during the e-meeting on the basis of the two-minute reports.
The regular group e-meetings will be on Tuesday, 20 September and Tuesday, 27 September at 8 pm.
As part of the prior assignment you were to have selected a reference manager and to have started using it. Be sure that the link to your
annotated bibligraphy is on your blog. E-mail the instructor immediately if you are having any difficulty setting this up.
Working within your chosen focus topic, go to scholar.google.com and find a different recent paper in your focus topic that is accessible
to you immediately, read that paper and and using scholar.google.com, the library any any other research resources you can find, prepare a
list of at least three seminal papers for your research topic. A seminal paper is one that started an important thread in the research topic.
It may be from years, decades or centuries in the past. As such, it may be difficult to obtain quickly. Therefore you should select your
seminal papers immediately, so you will have time to get and read at least one of them in the time-frame of this assigment. Having selected
your recent paper that is accessible to you immediately, also select one of your seminal papers that is available to you no later than by
Tuesday, 27 September 2016. You may need to use RIT library's
interlibrary loan service. ...
Prepare your 5th and 6thpapers and presentation, one recent based on the recent paper and one based on the seminal paper, one to be ready
by the 27th and one by the 4th.
You are reminded that you are not simply to regurgitate what you read in your selected papers. You are to do substantial reading and
research so that you actually understand what you are discussing. This requirement to do research applies not only to recent papers, but to
seminal papers as well. Even a paper that started a thread of research has some context within which it was created, You must present the
state of the field in which the work was being done, and how this paper fits in and what it contributes. You must be _very_ careful not to
cut and paste or simply paraphrase the text of the paper, but to engage your brain and put in the time and effort to do a proper critical
review of the paper you choose. If you are unable to do a decent job on the first paper you choose, choose a different paper.
The presentation must be exactly 15 slides, beginning with a title slide and ending with a references slide, leaving you 13 slides in
which to tell a coherent scientific story. Don't jam too much material onto each slide. These constraints may seem artificial and daunting,
but learning to cope with them is important.
The paper must be a properly structured paper with real content, reflecting real research. It will take you 9-12 hours of intensive work
to do this even if nothing goes wrong. The paper should reflect that level of effort.
Describe everything you have done for this course up to this point in your course blog. Be sure to include links to your
papers and presentations. Email the url of your blog to the instructor.
Assignments 7 and 8: Assigned, Tuesday 4 October 2016; due Thursday 13 October 2016 and Tuesday 18 October 2016.
Note: This is a double assignment to allow sufficient time for an inter-library loan. In this assignment, one of the papers you
will review may not be immediately accessible and you may need time for an inter-library loan.
Be sure to complete assignments 1 - 6 above, especially getting your blog started and getting ready to present. Have a coherent timed
two-minute report on what you have done for this course ready to present. Have a single slide ready. Every student will present their slide,
and at each group e-meeting, at least two students will also present one of the presentations they have worked on. The choice of which
students present will be made during the e-meeting on the basis of the two-minute reports.
The regular group e-meetings will be on Tuesday, 4 October, but the next group e-meeting would have conflicted with the Jewish holiday of
Yom Kippur, so there will be a group e-meeting on Thursday 13 October at 10 pm rather than at 8 pm.
I would like to give each of you a fair evaluation of your progress for the semester after these two assignments and to add a list of
all your blogs, presentations, papers and partially completed annotated bibliographies to the course web page, both as an aid in evaluting
your own work and to provide a valuable resource for the other students. Therefore please be sure to get everything you have done for this
course in as good shape as you can for evalution by 10 am on 18 October 2016 with all necessary links for that evaluation gathered into one
blog entry and send the URL for your blog in an email to me both for evaluation and for posting for the class.
Working within your chosen focus topic, go to scholar.google.com and find a different recent paper in your focus topic that is
accessible to you immediately, read that paper and and using scholar.google.com, the library any any other research resources you can find,
prepare a list of at least three seminal papers on algorithms or software that is essential to your research topic. A seminal paper is one
that started an important thread in the research topic. It may be from years, decades or centuries in the past. As such, it may be difficult
to obtain quickly. By restricting to topic of the seminal paper to algorithms or software essential to your research topic, we have made is
even harder to get a paper on time. Therefore you should select your seminal papers on software or algorithms immediately, so you will have
time to get and read at least one of them in the time-frame of this assigment. If you happened to choose a software or algorithms paper for
assignments 5 and 6 and prepared slides and a paper on it, you must choose a different paper to prepare this time. Having selected your
recent paper that is accessible to you immediately, also select one of your seminal papers that is available to you no later than by
Thursday, 13 October 2016. You may need to use RIT library's interlibrary loan service. ...
Prepare your 7th and 8th papers and presentation, one based on the recent paper and one based on the seminal paper, one to be ready by
the 13th and one by the 18th.
You are reminded that you are not simply to regurgitate what you read in your selected papers. You are to do substantial reading and
research so that you actually understand what you are discussing. This requirement to do research applies not only to recent papers, but to
seminal papers as well. Even a paper that started a thread of research has some context within which it was created. You must present the
state of the field in which the work was being done, and how this paper fits in and what it contributes. You must be _very_ careful not to
cut and paste or simply paraphrase the text of the paper, but to engage your brain and put in the time and effort to do a proper critical
review of the paper you choose. If you are unable to do a decent job on the first paper you choose, choose a different paper.
The presentation must be exactly 15 slides, beginning with a title slide and ending with a references slide, leaving you 13 slides in
which to tell a coherent scientific story. Don't jam too much material onto each slide. These constraints may seem artificial and daunting,
but learning to cope with them is important.
The paper must be a properly structured paper with real content, reflecting real research. It will take you 9-12 hours of intensive work
to do this even if nothing goes wrong. The paper should reflect that level of effort.
Describe everything you have done for this course up to this point in your course blog. Be sure to include links to your
papers and presentations. Email the url of your blog to the instructor.
Assignments 9 and 10: Assigned, Tuesday 18 October 2016; due Tuesday 25 October 2016 and Tuesday 1 November 2016.
IMPORTANT REMINDER: Each of you should have updated your blog and emailed me the URL by 10 am on Tuesday
18 October 2016 so that URL can be posted on the course web page for all the students in the class to see and use.
If you have not done so yet, please do so immediately.
Note: This is a double assignment to allow sufficient time for an inter-library loan. In this
assignment, one of the papers you will review may not be immediately accessible and you may need time for
an inter-library loan.
Working within your chosen focus topic, go to scholar.google.com and find a different recent paper
in your focus topic that is accessible to you immediately, read that paper and and using scholar.google.com,
the library any any other research resources you can find, prepare a list of at least three
recent papers on data mining, databases, algorithms or software that is essential to your research topic.
You must choose different papers from the ones you chose previously. Note that the recent data mining, databases,
algorithms or software papers do not have to be immediately accessible, but if they are not you should get started
on trying to obtain them immediately.
Prepare your 9th and 10thpapers and presentation, one based narrowly focused on your research
topic and one data mining, databases, algorithms or software paper that is essential to your research topic, and one to
be ready by the 25th and one by the 1st.
You are reminded that you are not simply to regurgitate what you read in your selected papers.
You are to do substantial reading
and research so that you actually understand what you are discussing. This requirement to do research applies not only
to recent papers, but to seminal papers as well. Even a paper that started a thread of research has some context within
which it was created, You must present the state of the field
in which the work was being done, and how this paper fits in and what it contributes. You must be _very_ careful not to cut and
paste or simply paraphrase
the text of the paper, but to engage your brain and put in the time and effort to do a proper critical review of the
paper you choose.
If you are unable to do a decent job on the first paper you choose, choose a different paper.
The presentation must be exactly 15 slides, beginning with a title slide
and ending with a references slide, leaving you 13 slides in which to tell a coherent scientific story. Don't jam too
much material onto each slide. These constraints may seem artificial and daunting, but learning to cope with them is
important.
The paper must be a properly structured paper with real content, reflecting real research. It will take you 9-12 hours
of intensive work to do this even if nothing goes wrong. The paper should reflect that level of effort.
Describe everything you have done for this course up to this point in your course blog. Be sure to include links to your
papers and presentations. Email the url of your blog to the instructor.
Assignments 11 and 12: Assigned, Tuesday 1 November 2016; due Tuesday
8 November 2016 and Tuesday 15 November 2016.
1. For the first part of this asignment, you are to review the work
of each of your classmates to date by looking at the list of student names
and blog URLs in the RIT course web page for this course (BIOL63501.2161)
Content tab Blog Links module. You are to grade yourself using the same
standards as you apply to your classmates. This is the same thing you were
supposed to do in a prior assignment given you by email. Many of you did
not have your work ready then. You are entering the last month of the
semester. It is time to get caught up on all your work. In this grading
pass, you may refer to what you did previously, but just as you will have
updated your work, your classmates hopefully will have updated theirs, so
be sure to base your grade on what is there now, not what was there
previously. You are to compose an email to me (not to anybody else) with a
letter grade (A, B, C or F) and a short one sentence evaluation for each
student listed. The main issue you should evaluate is the depth of the
background research done so far for the semster as demonstrated in the
critical bibliography (if provided) or in the last 3 papers (if provided).
YOU will be evaluated on your skill and honesty in doing these
evaluations. You are not to post these evaluations on your blog or
web page. You are to include an evaluation of yourself in your
submission. I will "blind" your evaluations and give a summary of the
overall results to each student, but your evaluation will not be
seen under your name by anybody other than me. This evaluation is so
important it takes the place of one paper. You are to submit you response
to this assignment by 10 am on Tuesday 8 November 2016.
2. It is now time to get started on your final presentation and paper
for the semester. As described in the syllabus "For the end of the
course you will prepare a full length paper. This may be created from
prior short papers or be something new. In any case you should prepare a
well-researched paper as well as a set of 45 PowerPoint slides.". To
get you started on this difficult task, you are to prepare a 15 slide
discussion presentation of the focus for your final presentation in which
you give a 10-slide background section containing a preliminary timeline
discussing the topic you are bringing together, and a 5-slide outline of
the organization you plan for the final talk. The paper that you create
to go with the slides is to include a thorough bibliography on your topic
and a discussion of the outline. The style you are to use for this week
is that of the IUCr Acta Crystallographica http://journals.iucr.org/a/services/authorservices.html.
This part of the assignment is due by 10 am on Tuesday 15 November 2016.
For the e-meeting on 8 November, you will have one last chance to catch up
of presentations, especially seminal paper presentations.
3. In order to understand what you need to do in the final
presentation and paper, be sure to attend the e-meetings this Tuesday, 1
November, as well as Tuesday, 8 November. After that, if you hope to
complete the course within the semester, you will need to be working on
final presentation assignments.
4. You will each be getting an email from me giving you a preliminary
estimate of your standing in this course by the e-meeting on Tuesday 1
November 2016, based both on the work I have seen and the preliminary
grading by your classmates. If you do not have your own evaluation by
then, please contact me promptly.
Assignments 13, 14 and 15: Assigned, Tuesday 15 November 2016; due
Tuesday 22 December 2016, Tuesday 29 November 2016, and Tuesday 6 December
2016.
1. As will have been discussed in the e-meetings, you are now to work
on the details of the 30 slide part of your final presentation, telling a
compelling story about your focus topic. By Tuesday 22 November, you are
to flesh out the outline presentation you prepared with a more detailed
paper giving a parapraph of text for each bullet point in your slides.
You may revise your slides as you do this.
2. By Tuesday 29 November, you are to have prepared a preliminary
version of your complete final presentation for my review and (ungraded)
comments, along with a list of your dates and hours of availability for
two events: presentation of your final presentation online between 6 and
9 December, and taking of an online final exam between 12 December and
16 December.
3. Promptly by 10 am Tuesday 6 December, you are to have prepared a
final version of your complete final presentation and paper for grading
and caught up on everything else you owe for this course that you hope to
have incuding in grading other than actually doing your final presentaion
and taking the final exam and posted all necessary links to your
blog.
4. If you do not have everything to consider for grading other
than actually doing your final presentaion and taking the final exam ready
by 10 am on Tuesday 6 December, you are advised to contact me immediately
to discuss what to do, including the possibility of taking an
incomplete.
