BOL: Related items

Look up a biological numbers

Jitendra Narayan — Fri, 23 Aug 2013 03:27:45 -0500

Did you ever need to look up a number like the volume of a cell or the cellular concentration of ATP, only to find yourself spending much more time than you wanted on the Internet or flipping through textbooks - all without much success?

Well, it didn’t happen only to you. It is often surprising how difficult it can be to find concrete biological numbers, even for properties that have been measured numerous times. To help solve this for one and all, BioNumbers (the database of key numbers in molecular biology) was created. Along with the numbers, you'll find the relevant references to the original literature, useful comments, and related numbers.

To cite BioNumbers please refer to: Milo et al. Nucl. Acids Res. (2010) 38: D750-D753. When using a specific entry from the database it is highly recommended that you also specify the BioNumbers 6 digit ID, e.g. "BNID 100986, Milo et al 2010".

Address of the bookmark: http://bionumbers.hms.harvard.edu/

Bioclues and Pine Biotech join forces to advance Bioinformatics in India

eliabrodsky — Fri, 14 Jun 2019 10:20:47 -0500

As a collaborative effort, the two organizations will help implement best practices in bioinformatics education across universities in Inida that have little to no experience in bioinformatics. The collaboration comes as Pine Biotech starts registrations for it's pilot program at Amity University in Kolkata, India.

To read more about this collaboration, visit: https://edu.t-bio.info/pine-biotech-joins-forces-with-the-bioclues-organization-to-promote-bioinformatics/

Ancestor at work !!!

Jit — Sun, 25 Aug 2013 19:45:28 -0500

When they will learn Bioinformatics :)

Liu Lab

Tue, 04 Feb 2020 06:27:02 -0600

Shirley is a computational biologist with expertise in cancer epigenetics. Her research focuses on algorithm development and integrative mining from big data generated on microarrays, massively parallel sequencing, and other high throughput techniques to model the specificity and function of transcription factors, chromatin regulators and lncRNAs in tumor development, progression, drug response and resistance.

https://liulab-dfci.github.io/software/

Chang lab

Tue, 24 Sep 2013 17:25:49 -0500

The Chang lab is focused on how the activities of hundreds or even thousands of genes (gene parties) are coordinated to achieve biological meaning. We have pioneered methods to predict, dissect, and control large-scale gene regulatory programs; these methods have provided insights into human development, cancer, and aging. A particular interest is how cells know and remember their locations in the body, particularly with the help of long noncoding RNAs.

More at http://changlab.stanford.edu/index.html

NGSymposium in Computational Biology

Mon, 09 Mar 2020 06:00:30 -0500

We have a great pleasure to invite you to the NGSymposium in Computational Biology to celebrate the 5th anniversary of the NGSchool Summer Schools. This international conference will make way for exchanging knowledge and experiences between experienced and early-stage researchers as well as bioinformaticians. The meeting will be held on 31.07 - 1.08.2020 in Warsaw. It will be a satellite event to the #NGSchool2020: Statistical Learning in Genomics. It will cover a wide range of topics from basic and applied biomedical sciences: bioinformatics, genomics, transcriptomics, computational biology, Machine Learning.

Registration of active participants will be open from February, 27 12 PM CET to April 17, 23:59 CET. In registration forms you will be asked for providing us with some basic information about yourself. You will also be able to submit your abstract. You can save your registration form after filling it partially and come back later to supply more data e.g. upload an abstract. Your registration will be completed only with the payment of the registration fee reaching our accounts - please make sure to transfer the money in advance!

Registration of passive participants will be open after closing of registration of active participants.

Details an registration: https://ngschool.eu/conference/

Genetics for Fun and Profit: Andrew Hessel at TEDxVilnius

Sun, 01 Sep 2013 19:15:06 -0500

Andrew Hessel co-chairs the Bioinformatics and Biotechnology track at the Singularity University, an institution founded by futurist Ray Kurzweil and X Prize Foundation CEO Peter Diamandis, with sponsorship from world-leading organizations that include Google, Autodesk, and NASA. He is also the founder of the Pink Army Cooperative, a venture aiming to make open source personalized cancer therapies. His work has been featured in The New York Times, Futurist Magazine, H+, and Wired News. In the spirit of ideas worth spreading, TEDx is a program of local, self-organized events that bring people together to share a TED-like experience. At a TEDx event, TEDTalks video and live speakers combine to spark deep discussion and connection in a small group. These local, self-organized events are branded TEDx, where x = independently organized TED event. The TED Conference provides general guidance for the TEDx program, but individual TEDx events are self-organized.* (*Subject to certain rules and regulations)

Frequent parameters for bioinformatics tools !

BioStar — Tue, 27 Oct 2020 19:42:32 -0500

Third party executable parameters and options.

Trimmomatic

“ILLUMINACLIP:...:2:30:10”

“LEADING:15”

“TRAILING:15”

“SLIDINGWINDOW:4:20”

“MINLEN:20”

“TOPHRED33”

Filtlong

--min_length 500

--min_mean_q 85

--min_window_q 65

FastQ Screen

--aligner bowtie2' (bwa for PacBio)

--subset 1000 (for PacBio)

SPAdes

--careful

--disable-gzip-output

--cov-cutoff auto

--phred-offset 33

HGAP

Pbalign.task_options.min_accuracy: 70

Pbalign.task_options.no_split_subreads: false

Genomic_consensus.task_options.min_confidence: 40

falcon_ns.task_options.HGAP_GenomeLength_str:

6000000

Pbcoretools.task_options.read_length: 0

Genomic_consensus.task_options.use_score: 0

Pbalign.task_options.min_length: 50

Pbalign.task_options.algorithm_options: --minMatch 12

--bestn 10 --minPctSimilarity 70.0

Pbalign.task_options.hit_policy: randombest

Pbcoretools.task_options.other_filters: rq >= 0.7

Pbalign.task_options.concordant: false

Genomic_consensus.task_options.min_coverage: 5

falcon_ns.task_options.HGAP_SeedCoverage_str: 30

falcon_ns.task_options.HGAP_AggressiveAsm_bool: false

Genomic_consensus.task_options.algorithm: best

falcon_ns.task_options.HGAP_SeedLengthCutoff_str: -1

Genomic_consensus.task_options.diploid: false

MeDuSa

-random 100

Prokka

--usegenus

--force

--addgenes

--rfam

--rawproduct

cmsearch (taxonomy, 16S)

--rfam

--noali

blastn (taxonomy, 16S)

-evalue 1E-10

blastn (MLST)

-ungapped

-dust no

-evalue 1E-20

-word_size 32

-culling_limit 2

-perc_identity 95

blastp (VF)

-culling_limit 2

RGI (ABR)

--input_type contig

bowtie2 (mapping)

--sensitive

minimap2 (mapping)

-a

-x map-ont

samtools mpileup (SNP detection)

-uRI

bcftools call (SNP detection)

--variants-only

--skip-variants indels

--output-type v

--ploidy 1

-c

SNPsift filter (SNP detection)

"( QUAL >= 30 ) & (( na FILTER ) | (FILTER = 'PASS')) &

( DP >= 20 ) & ( MQ >= 20 )"

SNPeff ann (SNP detection)

-nodownload

-no-intron

-no-downstream

-no SPLICE_SITE_REGION

-upDownStreamLen 250

bcftools consensus

(phylogenetic tree)

--haplotype 1

fasttreemp

-nt

-boot 100

roary

-e

-n

-cd 100

-g 100000

PostDocs positions in computer science in HELSINKI, FINLAND

Fri, 06 Sep 2013 10:11:19 -0500

Several university departments in the Helsinki region, Finland, are looking for postdoctoral researchers in the field of computer science and information technology. Jobs are available at:
· Helsinki Institute for Information Technology HIIT, Aalto University and University of Helsinki, http://www.hiit.fi
· Department of Computer Science, University of Helsinki, http://www.cs.helsinki.fi
· Department of Information and Computer Science, Aalto University, http://ics.aalto.fi
· Department of Computer Science and Engineering, Aalto University, http://cse.aalto.fi
· Department of Mathematics and Statistics, University of Helsinki, http://mathstat.helsinki.fi/english/

Why Helsinki?
The collaborating Aalto University and University of Helsinki form a leading hub of computer science and modelling, including Machine learning, Data mining, Algorithms, Computational Logic, Cloud computing, Distributed computing, Human-centric ubiquitous ICT, Bioinformatics, etc.
Helsinki region is a safe, pleasant and attractive place to live in, with well-functioning services such as public transport etc. Finland has a comprehensive social security and health care system, including exceptionally good parental leaves, and children's day care services.

Positions are offered in:
Algorithm engineering (String Algorithms group)
Algorithmic bioinformatics (Genome-Scale Algorithmics group)
Automated reasoning and search, especially propositional logic (Computational Logic group)
Computational astrophysics and/or data analysis (Computational Methods and Data Analysis for Astrophysics group)
Computational biology and statistical methods in bioinformatics (Computational Systems Biology group)
Computational creativity and data mining (Discovery group)
Dynamic and large-scale networked systems (Data Communications Software group)
Intelligent multimodal information access (Content-Based Image and Information Retrieval Group)
Machine learning and neuroscience (Statistical Machine Learning group)
Machine learning for structured data (Kernel Machines, Pattern Analysis and Computational Biology group)
Machine learning methods for infectious disease epidemiology (Bayesian Statistics Group)
Probabilistic modeling and machine learning (Complex Systems Computation group)
Statistical machine learning (Statistical Machine Learning group)
Analysing ubiquitous sensor data (HIIT-Wide Focus Area)
Interactive visualization (HIIT-Wide Focus Area)
Affective computing and BCI (HIIT-Wide Focus Area)
Intelligent user interfaces and/or recommender systems (HIIT-Wide Focus Area)
Information retrieval and HCI (HIIT-Wide Focus Area)
Machine learning and data analysis, especially information retrieval, HCI, text and context data (HIIT-Wide Focus Area)
Probabilistic modeling and data analysis for bioinformatics (HIIT-Wide Focus Area)

More at http://www.hiit.fi/postdoc-call-2013

Common Bioinformatics Interview Questions !

Jit — Sat, 23 Jan 2021 06:07:50 -0600

The possibility of an interview for a bioinformatics position in the life sciences may be very disquieting, but the same concerns emerge time and again in my experience. So, it is exceedingly worthwhile to plan for future bioinformatics interview questions. Doing this will really give you the advantage in obtaining the position.

The following 5 questions are those that I have heard many times during the job-search process. There is no reason for not planning responses in such situations.

1. Tell Us About Yourself
This is a very typical opener in interviews. It's a perfect question to ask, and getting something planned will really help you concentrate and ease in the conversation. However, you need to make sure that your response is applicable to the job you're interviewing.
It's probably better to keep your answer professional. Try to include these in the answer as well: where did your love of science and bioinformatics come from? How the heck did you end up in this field? Why programming and scripting ?

2. What is your plan for your bioinformatics career? / How do you look at yourself in five years? / How are your personal objectives to accomplish these goals / What are the plan for your research fundings ?

Your CV/resume has already impressed the selection panel if you have been invited for an interview. The questions from the bioinformatics interview team provide an incentive for you to market yourself and illustrate the work in question with the most appropriate knowledge.

3. What do you understand about the job description/What would your suggested research path be if you were a successful candidate?
Summarize the specifics of the advertised bioinformatics position in your own words. Follow on with some suggestions of how you want to extend your research and create your own projects within the community.

4. Will you work as a group or do you want to work on your own?
This requirement can vary from jobs to job, so when addressing, be alert. A company/research PI may need a bioinformatician that is able to work on a single project autonomously, or they may need a person who can help direct and organize a team. In your response, refer to the job description.

5. What particular methods have you used to date with your experiments?
You might have experience with all the laboratory techniques described in the job description, but stress the ones you highly experienced with. Highlight your professional abilities and stress that you are extremely capable of mastering new techniques with others ...

At the end of the day, remember that you're questioning the jury as well as they're interviewing you. You will ought to think of any questions you would like the interview panel to pose. This indicates that you have done your homework and serious about the position.

All the best for your future job interview.