This is the assignments page for BIOL.635.01 - Bioinformatics Seminar (BIOL63501.2151), an online course at
Rochester Institute of Technology, for Fall 2015. 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 Sunday evenings to be available by
the following Mondays.
Assignment 1: Assigned, Monday 24 August 2015; due Monday 31 August 2015.
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 BIOL635F15, e.g. http://yayahjbBIOl635F15.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, 27 August 2015, 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, Monday 31 August 2015; due Monday 7 September 2015.
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 an 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.
Note: Monday 7 September is an RIT holiday, so you will be considered to have completed assignment 2 on time if you email
your work early on Tuesday, 8 September.
Assignment 3: Assigned, Monday 7 September 2015; due Monday 14 September 2015.
Note: Monday 7 September is an RIT holiday, so it is fine to start work on this assignment on Tuesday, 8 September.
1. Be sure to complete assignments 1 and 2, 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 two assignments.
The regular group e-meeting will be on Thursday, 10 September at 8 pm. The alternate
group e-meeting will occur before that, on Tuesday, 8 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 at each group
e-meeting, at least two students 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.
2. I will be providing written feedback on the work you have submitted thus far during
this week. 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 morning. It would be unfair to the students who have kept up to delay any longer
than that.
3. 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 ...
4. 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.
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 an 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. 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 4: Assigned, Monday 14 September 2015; due Monday 21 September 2015.
Note: The Jewish New Year, Rosh Hashanah, is observed from sundown Sunday 13 September 2015
through sundown Tuesday, 15 September, which overlaps both with the due date of the prior assignment and
with getting started on this assignment. If you observe this holiday, please either submit assignment 3
and get started on assignment 4 before Sunday evening, or after sunset on Tuesday. It is still your obligation to
complete assignment 4 by the morning of Monday 21 September.
1. 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 Thursday, 17 September at 8 pm. The alternate
group e-meeting will occur before that, on Tuesday, 15 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 at each group
e-meeting, at least two students 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.
2. By Monday 21 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.
3. 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 ...
4. 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 interms 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 an 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 9-12 hours
of intensive work to do this even if nothing goes wrong. The paper should reflect that level of effort.
8. 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.
Assignments 5 and 6: Assigned, Monday 21 September 2015; due Monday 28 September 2015 and Monday 5 October 2015.
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.
Note: The Jewish Day of Atonement, Yom Kippur, is observed from sundown Tuesday 22 September 2015
through sundown Wednesday, 23 September 15. Therefore, there will be no alternate group e-meeting on Tuesday meeting.
The only group e-meeting this week will be on Thursday.
1. 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, 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.
2. 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.
3. 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 Monday, 28 September
2015. You may need to use RIT library's interlibrary loan service.
...
4. Prepare your 5th and 6thpapers and presentation, one recent based on the recent paper and
one based on the seminal paper, on to be ready by the 28th and one by the 5th.
5. 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 an 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 9-12 hours
of intensive work to do this even if nothing goes wrong. The paper should reflect that level of effort.
8. 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.
Assignments 7 and 8: Assigned, Monday 5 October 2015; due Tuesday 13 October 2015 and Monday 19 October 2015.
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.
Note: The RIT academic calendar treats Monday, 12 October as a holiday, and puts Tuesday, 13 October on
a Monday scedhule. Therefore the assignment 7 portion of this double assignment is due first thing the morning of
Tuesday, 13 October. However, we will still offer an alternate group e-meeting that evening at 8 pm/
1. Be sure to complete assignments 1 - 6 above. 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 19 October 2015 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.
2. 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 Tuesday, 13 October
2015. You may need to use RIT library's interlibrary loan service.
...
3. Prepare your 7th and 8thpapers 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 19th.
4. 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 an 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.
5. 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. 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.
7. 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.
Assignments 9 and 10: Assigned, Monday 19 October 2015; due Monday 26 October 2015 and Monday 2 November 2015.
IMPORTANT REMINDER: Each of you should have updated your blog and emailed me the URL by 10 am on Monday
19 October 2015 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.
Note: Because of low attendance at the Tuesday alternate e-meeting, in the immediately future, we will only
have an e-meeting on Thursdays at 8 pm. If you need the Tuesday meetings restored, please send an email request at
least one week in advance.
1. 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 me immediately accessible, but if they are not you should get started
on trying to obtain them immediately.
2. 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 26th and one by the 2nd.
3. 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 an 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.
4. 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.
5. 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.
6. 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.
Assignments 11 and 12: Assigned, Monday 2 November 2015; due Monday 9 November 2015 and Monday 16 November 2015.
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 (BIOL63501.2151) Content tab Blog Links module.
You are to compose an email to me (not to anybody else) with a letter grade (A, B 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 Monday
9 November 2015.
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 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 Monday 16 November 2015.
3. In order to understand what you need to do in the final presentation and paper, be sure to attend the e-meeting this
Thursday, 5 November.
4. You will each be getting an email from me giving you a preliminary estimate of your standing in this course by the end of
the day on Monday 2 November 2015. If you do not have your own evaluation email by Tuesday 3 November 2015, please contact me
promptly.
Assignments 13, 14 and 15: Assigned, Monday 16 November 2015; due Monday 23 November 2015, Monday 30 November 2015, and
Monday 7 December 2015.
1. As discussed in the last e-meeting, 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 Monday 23 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 you slides as you do this.
2. By Monday 30 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 7 and 10 December, and taking of an online final exam between 11 December and 18 December.
3. Promptly by 10 am Monday 7 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 Monday 7 December, you are advised to contact me immediately
to discuss what to do, including the possibility of taking an incomplete.
WATCH THIS SPACE FOR ONE FUTURE ASSIGNMENT -- THE POSTING OF THE SCHEDULE FOR THE FINAL PRESENTATIONS AND FINAL EXAM
