News
Feedback conversations and seminar closingWritten on 13.07.23 by Andre Holzer Dear Students,
Dear Students,
To provide you with the best possible educational experience, I would like to invite you to participate in a personal feedback conversation. For this matter, please come to my office (E2.1 room 107) tomorrow 14.07 between 1-3 pm. You also have the option to call via Teams during these hours, yet I recommend being there in person. As part of the 1-to-1 conversations, we will discuss the overall outcomes of the seminar, provide you with your grades and give you detailed feedback on your report, review, and presentation.
Best regards, |
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Written on 22.06.23 (last change on 22.06.23) by Andre Holzer Dear Students,
With less than one week to go we hope you all have made good progress in preparing your presentations. Please be reminded to send a copy of your final slides via E-Mail to andre.holzer@uni-saarland.de by Tuesday 27th.
Please make sure to arrive in time and be reminded… Read more Dear Students,
With less than one week to go we hope you all have made good progress in preparing your presentations. Please be reminded to send a copy of your final slides via E-Mail to andre.holzer@uni-saarland.de by Tuesday 27th.
Please make sure to arrive in time and be reminded to match the presentation guidelines and requirements laid out during the kick-off meeting.
We look forward to an exciting day full of inspiring talks on Nanopore and PacBio sequencing. In the meantime, if you have any concerns or require further assistance, please do not hesitate to reach out.
PS: For those that have dropped out but are still interested in the topic, please feel free to attend the conference day and engage in the discussions. |
Presentations and Conference day 28.06Written on 05.06.23 by Andre Holzer Dear Students,
For the final part of the seminar please have a look at the reviews to your individual reports and make sure to use the comments and criticism to improve your material for the presentation of your topic and paper. Wednesday 28th June will be the day of our conference. The five… Read more Dear Students,
For the final part of the seminar please have a look at the reviews to your individual reports and make sure to use the comments and criticism to improve your material for the presentation of your topic and paper. Wednesday 28th June will be the day of our conference. The five talks will be distributed in two sessions: 10:30-12:30and 13:30-16:30. Thus, please send me a final copy of your slides via E-Mail by Tuesday 27th and make sure to arrive in time, we will start 10:10 am.
I will send out a detailed schedule for the conference sooner to the day. As for the length, content, and structure of your talk, be reminded of the details from the kick-off meeting. If you have any concerns or require further assistance, please do not hesitate to reach out. Your success in this course is of importance to us.
We look forward to an exciting day full of inspiring talks on Nanopore and PacBio sequencing.
PS: For those that have dropped out but are still interested in the topic, please feel free to attend the conference day and engage in the discussions. |
Important Update: Paper Assignment and Extended Report DeadlinesWritten on 10.05.23 by Andre Holzer Dear Students,
I hope this email finds you well. I wanted to inform you of an important update regarding the paper assignments for the seminar and remind you of the deadline to hand in your reports. Firstly, the topic/paper assignments are fixed now and especially for those of you who have… Read more Dear Students,
I hope this email finds you well. I wanted to inform you of an important update regarding the paper assignments for the seminar and remind you of the deadline to hand in your reports. Firstly, the topic/paper assignments are fixed now and especially for those of you who have not assigned themselves a topic please look them up via the topics spreadsheet linked in the Materials section. You will find the assignments for the review part there too. Secondly, to allow you a bit more time for the preparation of the reports and reviews, we have decided to extend the deadlines by two days. The new deadlines are as follows:
Please ensure that you submit your reports by the respective deadlines mentioned above. Late submissions will not be accepted, as we need sufficient time to review and provide feedback on your work. Finally, be reminded that you will have to register via LSF until May 16th to get credits for the seminar. If you have any questions, please do not hesitate to reach out. With that said, be reminded, I will not be in Saarbrücken next week (ONT conference is calling ;)) thus there will not be any more consultation hours until the reports are due.
Best regards, Dr Andre Holzer |
Reminder: Select your topicWritten on 02.05.23 by Andre Holzer Dear all, With the de-registration decline now passed, I am pleased to announce that a cohort of 10 students is taking the seminar this semester. For those of you who have not registered for the exam via LSF, please do so ASAP. Although we won't have a classical exam you will have to sign up… Read more Dear all, With the de-registration decline now passed, I am pleased to announce that a cohort of 10 students is taking the seminar this semester. For those of you who have not registered for the exam via LSF, please do so ASAP. Although we won't have a classical exam you will have to sign up for the exam (exam number 10184) via LSF to get credits for the seminar. Further we have 5 out of 10 people who have successfully assigned themselves a topic/paper using the following link. For all others, you will have time until tomorrow evening to select one yourself or I will assign you one. Best wishes, Andre
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Kick-off meeting: April 25th at 2:30-4pmWritten on 20.04.23 (last change on 22.06.23) by Andre Holzer Our kick-off meeting will be held on April 25th at 2:30-4pm at the ZBI E2.1 in room 106. During this mandatory meeting, we will introduce the seminar schedule and expectations, assign topics/papers, and discuss how we will be approaching the seminar material. We will also answer any questions you… Read more Our kick-off meeting will be held on April 25th at 2:30-4pm at the ZBI E2.1 in room 106. During this mandatory meeting, we will introduce the seminar schedule and expectations, assign topics/papers, and discuss how we will be approaching the seminar material. We will also answer any questions you may have about the seminar and the technologies covered. We encourage all students to participate actively in the seminar, as this will be a great opportunity to expand your knowledge and expertise in this exciting field. We also recommend that you familiarize yourself with the basics of long-read sequencing technologies before the kick-off meeting, as this will help you to select a topic of interest. |
This is a block seminar for students in Bioinformatics offered during the Summer Term 2023
| Prerequisites | Students in Bioinformatics with a B.Sc. degree in Life Sciences; solid English in speaking and writing |
| Credits | 7 ECTS credits |
| Language | English |
| Registration | using the SIC Course Management system (CMS) |
| Main tasks | report writing, peer-review, presentation, group discussion |
| Structure | topics and papers will be allocated beginning of term; reports and reviews to be due mid of term, presentations to be given during a block seminar at the end of the lecture period |
General information
Overview
The field of long-read sequencing has undergone significant advances in recent years and has become increasingly important in genomic research.
This graduate seminar in Bioinformatics will delve into the latest developments of long-read sequencing, and teach students about the newest technologies, applications, and tools in the field. The seminar will cover a range of topics including the principles, challenges, and latest advancements centered around PacBio & Nanopore sequencing, alongside highlighting examples of adaptation in research and clinical settings.
Through guided literature research, scientific writing, comprehensive presentations and group discussions, participants will gain an in-depth understanding of the current state of the field. Moreover, the seminar will showcase how these methods are being used to tackle complex genomic issues, such as obtaining accurate genome assemblies, monitoring metagenomes, resolving structural variations, or characterising epigenetic modifications.
The seminar is designed for students in Bioinformatics with an interest in expanding their knowledge and expertise in the cutting-edge field of long-read sequencing and will be offered as a block seminar in the summer semester 2023.
Pre-requirements for participation
The seminar aims at master students in Bioinformatics who preferably have a B.Sc. degree in Life Sciences. Successful completion of the lectures Algorithms for Sequence Analysis or Single Cell Bioinformatics can be helpful and is recommended but not a pre-requisite. Good language skills are presumed as all communications will be in English.
Note: This seminar gives 7 CP. Thus, you should be willing to invest a corresponding amount of ~210 hours for the preparation of your seminar material during the lecture period.
Certificate requirements
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Independent development of the assigned topic
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Writing a scientific report explaining your topic and paper
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Short description and introduction to the topic followed by a detailed explanation of the technology and bioinformatic methodology (content of the paper and beyond) and a discussion of the limitations, challenges, and perspectives
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3-4 pages of text, excluding title (page), references, figures, tables etc.
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in paper style format and scientific language
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Adequate review work on a report from another seminar participant
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Successful presentation (in English):
- Talk: 45 minutes
- Discussion: 10-15 minutes during which you should be able to answer questions from the tutor(s)/audience
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Attendance to all presentations is mandatory and must be done in person. You are requested to actively contribute to the discussions.
Final grade
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30% influenced by the quality of the submitted topic & methodology report
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20% by your review work
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50% based on the given presentation & slides
Registration
The maximum number of registrations for the seminar is limited to 15 participants.
In order to be able to take part in the seminar, please register via the SIC Course Management system (CMS) by April 15th at the latest. Please provide information about your background/experience and a statement of motivation to attend this seminar. Personal attendance at the kick-off meeting is mandatory. It is not possible to reserve a topic in advance. The last day to cancel is April 30th.
Lecturer/Tutor
Key Dates
| Registration | until April 15th, 2023 HERE |
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| Kick-off meeting (includes selection of topics and papers) [mandatory] | mid/end April (will be determined via doodle poll) |
| Deadline to (de-)register from seminar* | April 30th, 2023 |
| Deadline to sign up via LSF [mandatory]** | Mai 16th, 2023 |
| Weekly consultation hour [optional]*** | every Wednesday between 3 and 4 pm |
| Submission deadline for reports [mandatory] | Mai 21th, 2023 new! |
| Submission deadline for reviews [mandatory] | June 4th, 2023 new! |
| Conference days (block seminar) [mandatory] | between 22nd -30th June (doodle poll) |
* If you want to de-register from the seminar, please send an email to andre.holzer@uni-saarland.de and cancel online using CMS.
** Mandatory for everyone who wants to get credits for the course.
*** If you would like to discuss questions regarding the topic, paper, report or presentation you can call in on the weekly consultation hour via Teams or email andre.holzer@uni-saarland.de to arrange a meeting in person.