22111:Course plan autumn 2024 - Revision history

Henni: /* Monday Dec 16 */

2024-12-02T08:21:38Z

Monday Dec 16

← Older revision		Revision as of 10:21, 2 December 2024
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	[https://teaching.healthtech.dtu.dk/material/22111/Vejledning-til-digital-eksamen-DE-DK-ENG-revideret-2023-.pdf Here is a guide] to the Digital Exam interface (in Danish and English).		[https://teaching.healthtech.dtu.dk/material/22111/Vejledning-til-digital-eksamen-DE-DK-ENG-revideret-2023-.pdf Here is a guide] to the Digital Exam interface (in Danish and English).

	The assignment will be accessible from '''~~XXX~~''' on Dec 16.		The assignment will be accessible from '''15:00''' on Dec 16.

	=== Checklist for computers ===		=== Checklist for computers ===

Henni: /* Tuesday Oct 8 — Protein structure, PDB & PyMOL */

2024-11-15T13:30:43Z

Tuesday Oct 8 — Protein structure, PDB & PyMOL

← Older revision		Revision as of 15:30, 15 November 2024
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	:'''Link to advanced course:'''		:'''Link to advanced course:'''
	::* [~~https~~://~~teaching.healthtech~~.dtu.dk/22117~~/index.php/22117_-_Protein_Structure_and_Computational_Biology~~ 22117 Protein Structure and Computational Biology]		::* [http://kurser.dtu.dk/course/22117 22117 Protein Structure and Computational Biology]

	:'''Software''' for installation: [https://pymol.org/ PyMOL]		:'''Software''' for installation: [https://pymol.org/ PyMOL]

Carol: /* Tuesday Oct 1 — BLAST */

2024-10-01T06:52:20Z

Tuesday Oct 1 — BLAST

← Older revision		Revision as of 08:52, 1 October 2024
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	:'''Curriculum:''' section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF: on DTU Learn).		:'''Curriculum:''' section 3.2.5 → 3.3 (i.e. pages 47-52) in Immunological Bioinformatics (PDF: on DTU Learn).
	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.
	:'''Exercise: [[Exercise:~~_BLAST2~~\|BLAST]]'''		:'''Exercise: [[Exercise:_BLAST3\|BLAST]]'''
	<!--		<!--
	:'''Extra material:'''		:'''Extra material:'''

Henni: /* Tuesday Oct 8 — Protein structure, PDB & PyMOL */

2024-09-16T11:07:41Z

Tuesday Oct 8 — Protein structure, PDB & PyMOL

← Older revision		Revision as of 13:07, 16 September 2024
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	::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]		::* [https://teaching.healthtech.dtu.dk/22117/index.php/22117_-_Protein_Structure_and_Computational_Biology 22117 Protein Structure and Computational Biology]

	:'''Software''' for installation: [https://pymol.org/2/ PyMOL]		:'''Software''' for installation: [https://pymol.org/ PyMOL]
	::'''Note:''' you will need the license file found at DTU Learn under this week's topic. The license is valid for a limited time. If you need PyMOL for educational purposes later in your studies, you can go to https://pymol.org/edu/index.php and register as a student to get your own license file (and if you don't receive an email after registering, write to help@schrodinger.com). However, if you need PyMOL to make figures for a scientific publication, you will have to pay for a license.		::'''Note:''' you will need the license file found at DTU Learn under this week's topic. The license is valid for a limited time. If you need PyMOL for educational purposes later in your studies, you can go to https://pymol.org/edu/index.php and register as a student to get your own license file (and if you don't receive an email after registering, write to help@schrodinger.com). However, if you need PyMOL to make figures for a scientific publication, you will have to pay for a license.
	:'''Exercises:'''		:'''Exercises:'''

Henni: /* Tuesday Sep 3 — Introduction & taxonomy */

2024-09-01T14:19:20Z

Tuesday Sep 3 — Introduction & taxonomy

← Older revision		Revision as of 16:19, 1 September 2024
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	:'''Lectures:'''		:'''Lectures:'''
	:* ''Introduction to the course, bioinformatics, and computers'' — Henrik Nielsen.		:* ''Introduction to the course, bioinformatics, and computers'' — Henrik Nielsen.
	:* ''Evolution and taxonomy'' — ~~Rasmus Wernersson~~.		:* ''Evolution and taxonomy'' — Carolina Barra Quaglia.
	:'''Slides:''' will be made available on DTU Learn.		:'''Slides:''' will be made available on DTU Learn.
	:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — Written by Anders Gorm Pedersen.		:'''Curriculum:''' [https://teaching.healthtech.dtu.dk/material/22111/PDF/Chapter2_Evolution.pdf Brief Introduction to Evolutionary Theory] — Written by Anders Gorm Pedersen.

Henni: /* Hand-ins */

2024-08-29T14:41:44Z

Hand-ins

← Older revision		Revision as of 16:41, 29 August 2024
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	As preparation for the computer-based exam, each participant or group must write a "'''logbook'''" with answers to the questions posed in the exercise guides. After the exercise, you should upload the logbook to DTU Learn.		As preparation for the computer-based exam, each participant or group must write a "'''logbook'''" with answers to the questions posed in the exercise guides. After the exercise, you should upload the logbook to DTU Learn.

	'''NB:''' It is possible to hand in as a group. We would ''much'' rather receive one group hand-in than a number of identical logbooks.		'''NB:''' All hand-ins are per definition group hand-ins. If you work alone, you must form a "group" of one person.
			<!-- It is possible to hand in as a group. We would ''much'' rather receive one group hand-in than a number of identical logbooks. -->

	You decide which software you prefer for writing the logbook — e.g. Microsoft Word, [http://www.libreoffice.org/ LibreOffice] (free), [http://www.openoffice.org/ Apache OpenOffice] (free), Pages for Mac, [https://docs.google.com/ Google Docs] or similar. You should be able to insert '''screenshots''' in the logbooks for documentation purposes. Microsoft Word has a built-in screenshot tool. Both Windows 10/11 and Mac OS also have dedicated screenshot tools.		You decide which software you prefer for writing the logbook — e.g. Microsoft Word, [http://www.libreoffice.org/ LibreOffice] (free), [http://www.openoffice.org/ Apache OpenOffice] (free), Pages for Mac, [https://docs.google.com/ Google Docs] or similar. You should be able to insert '''screenshots''' in the logbooks for documentation purposes. Microsoft Word has a built-in screenshot tool. Both Windows 10/11 and Mac OS also have dedicated screenshot tools.
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	'''Please do ''not'' copy the questions''' from the exercise guide to your logbook. The hand-in module on DTU Learn has a system for plagiarism detection, which will raise an alarm if significant portions of your hand-in are identical to documents found on the internet — and that includes the exercise guides.		'''Please do ''not'' copy the questions''' from the exercise guide to your logbook. The hand-in module on DTU Learn has a system for plagiarism detection, which will raise an alarm if significant portions of your hand-in are identical to documents found on the internet — and that includes the exercise guides.

			In case you don't finish the exercises Tuesday afternoon, there is still a chance to hand in — the deadline for handing in at Learn is '''Thursday at 13:00''' each week. The '''answers to the exercises''' will become visible at the same moment (Thursday at 13:00). You should read the answers carefully and compare with your own answers.

			We do not offer individual feedback on the hand-ins, but we will give a collective feedback before the lecture the next Tuesday, where we address any common mistakes there may have been.

	'''NB:''' ''The hand-ins do not affect your grade'' — they are mainly meant as a preparation for the exam. They are also a means for us to check the understanding of the teaching; if we can see that many participants have made the same mistake, we will try to explain the issue better at the beginning of the next lecture.		'''NB:''' ''The hand-ins do not affect your grade'' — they are mainly meant as a preparation for the exam. They are also a means for us to check the understanding of the teaching; if we can see that many participants have made the same mistake, we will try to explain the issue better at the beginning of the next lecture.

Henni: /* Tuesday Sep 10 — GenBank */

2024-08-29T08:58:31Z

Tuesday Sep 10 — GenBank

← Older revision		Revision as of 10:58, 29 August 2024
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	:'''Extra material:'''		:'''Extra material:'''
	:*[http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI)		:*[http://www.ncbi.nlm.nih.gov/books/NBK44863/ Entrez Sequences Quick Start] (NCBI)
	:*[https://doi.org/10.1093/nar/~~gkac1012~~ "GenBank ~~2023~~ update"] — article from the annual database issue of Nucleic Acids Research, ~~2023~~.		:*[https://doi.org/10.1093/nar/gkad903 "GenBank 2024 update"] — article from the annual database issue of Nucleic Acids Research, 2024.

	=== Tuesday Sep 17 — Translation & UniProt ===		=== Tuesday Sep 17 — Translation & UniProt ===

Henni: /* Tuesday Sep 3 — Introduction & taxonomy */

2024-08-29T08:56:02Z

Tuesday Sep 3 — Introduction & taxonomy

← Older revision		Revision as of 10:56, 29 August 2024
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	:'''Extra material'''		:'''Extra material'''
	:*"[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]" — Encyclopedia entry from 2009.		:*"[https://teaching.healthtech.dtu.dk/material/22111/ELS_bioinformatics.pdf Bioinformatics]" — Encyclopedia entry from 2009.
	:*"[https://doi.org/10.1093/nar/~~gkac1032~~ Database resources of the National Center for Biotechnology Information ~~in 2023~~]" — article from the annual database issue of Nucleic Acids Research, ~~2023~~		:*"[https://doi.org/10.1093/nar/gkad1044 Database resources of the National Center for Biotechnology Information]" — article from the annual database issue of Nucleic Acids Research, 2024

	=== Tuesday Sep 10 — GenBank ===		=== Tuesday Sep 10 — GenBank ===

Henni: /* Monday Dec 16 */

2024-08-23T08:59:02Z

Monday Dec 16

← Older revision		Revision as of 10:59, 23 August 2024
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	=== Monday Dec 16 ===		=== Monday Dec 16 ===
	'''Winter exam ~~2023~~:''' Go to https://eksamen.dtu.dk/ and find 22111.		'''Winter exam 2024:''' Go to https://eksamen.dtu.dk/ and find 22111.

	[https://teaching.healthtech.dtu.dk/material/22111/Vejledning-til-digital-eksamen-DE-DK-ENG-revideret-2023-.pdf Here is a guide] to the Digital Exam interface (in Danish and English).		[https://teaching.healthtech.dtu.dk/material/22111/Vejledning-til-digital-eksamen-DE-DK-ENG-revideret-2023-.pdf Here is a guide] to the Digital Exam interface (in Danish and English).

Henni: /* Tuesday Dec 3 — Bioinformatics in practice + old exam questions */

2024-08-15T10:07:24Z

Tuesday Dec 3 — Bioinformatics in practice + old exam questions

← Older revision		Revision as of 12:07, 15 August 2024
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	=== Tuesday Dec 3 — Bioinformatics in practice + old exam questions ===		=== Tuesday Dec 3 — Bioinformatics in practice + old exam questions ===
	:'''Lecture:''' ~~''TBA'' — TBA <!--"Real life case":~~ ''AI, phage discovery and rainforest genomics'' — Bent Petersen, KU. ~~-->~~		:'''Lecture:''' ''AI, phage discovery and rainforest genomics'' — Bent Petersen, KU.
	:'''Curriculum:''' (None - lean back and enjoy)		:'''Curriculum:''' (None - lean back and enjoy)
	:'''Slides:''' on DTU Learn.		:'''Slides:''' on DTU Learn.